Contents

1 Introduction

…

2 Setup script

The package OmicSelector has a lot of requirements that are nessesary to run all the experiments. The script below will allow to install most of them. It is highly recommended to install those packages using the code below.

If you are using our docker enviorment to learn this package you should not run this again. It would be a waste of time. [However, if you wish, you can play with the code in the notebook. Click here.](If you are using our enviorment to learn this package you can tweak this code in the interactive notebook. Click here.

Setup script:

readLines("setup.R") %>% paste0(collapse = "\n") %>% cat
#> install.packages(c("remotes","devtools"),repos = "http://cran.r-project.org")
#> install.packages(c("rlang","ps"), type = "source")
#> install.packages(c("roxygen2", "plotly", "rJava", "mice", "MatchIt", "kableExtra"))
#> install.packages("BiocManager",repos = "http://cran.r-project.org")
#> install.packages("plotly")
#> install.packages("reticulate")
#> library(BiocManager)
#> BiocManager::install(c("remotes","plyr","dplyr","edgeR","epiDisplay","rsq","MASS","Biocomb","caret","dplyr",
#>                        "pROC","ggplot2","DMwR", "doParallel", "Boruta", "spFSR", "varSelRF", "stringr", "psych", "C50", "randomForest",
#>                        "foreach","data.table", "ROSE", "deepnet", "gridExtra", "stargazer","gplots","My.stepwise","snow", "sva", "Biobase",
#>                        "calibrate", "ggrepel", "networkD3", "VennDiagram","RSNNS", "kernlab", "car", "PairedData",
#>                        "profileR","classInt","kernlab","xgboost", "keras", "tidyverse", "cutpointr","tibble","tidyr", "rpart", "party", "mgcv", "GDCRNATools",
#>                        "imputeMissings", "visdat", "naniar", "stringr", "doParallel", "R.utils", "TCGAbiolinks", "GDCRNATools", "kableExtra", "VIM", "mice", "MatchIt", "XML", "rmarkdown", "xtable", "ComplexHeatmap","circlize","BiocStyle","magick"))
#> remotes::install_github("STATWORX/bounceR", force = T)
#> #remotes::install_github("rstudio/reticulate")
#> remotes::install_github("Thie1e/cutpointr", force = T)
#> remotes::install_github("vqv/ggbiplot", force = T)
#> library(keras)
#> install_keras(method = "conda") # must have anaconda installed first, if not just use: install_keras()
#> 
#> 
#> install_github("kstawiski/OmicSelector") # Install our package.

This code does not cover the installation of mxnet, which can be used for benchmarking of the selected miRNA sets. The mxnet is however built and installed in our docker enviorment.

You can run this code directly from GitHub:

library(devtools)
source_url("https://raw.githubusercontent.com/kstawiski/OmicSelector/master/vignettes/setup.R")

As the OmicSelector package is installed we can load it easly.

library(OmicSelector)

3 Getting the data

To present the package functionality, we will use the pan-cancer data from TCGA (https://portal.gdc.cancer.gov/repository). These two commands below will download and store all the necessary data in your working directory. Please note, that this process may take some time (depending on your network connection), but has to be performed only once.

OmicSelector_download_tissue_miRNA_data_from_TCGA()
OmicSelector_process_tissue_miRNA_TCGA(remove_miRNAs_with_null_var = T)

Both of those function produce 2 files: tissue_miRNA_counts.csv and tissue_miRNA_logtpm.csv. First of those files contains metadata and raw counts as declared in TCGA. The second is are log-transformed transcripts-per-million (TPM) counts. Let’s load counts files and see its summary.

suppressWarnings(suppressMessages(library(data.table)))
suppressWarnings(suppressMessages(library(knitr)))
orginal_TCGA_data = fread("tissue_miRNA_counts.csv.gz")
orginal_TCGA_data[orginal_TCGA_data == ""] = NA
OmicSelector_table(table(orginal_TCGA_data$primary_site, orginal_TCGA_data$sample_type))
PrimaryTumor SolidTissueNormal
Adrenal gland 80 0
Bladder 409 19
Brain 512 5
Breast 1078 104
Bronchus and lung 991 91
Cervix uteri 307 3
Corpus uteri|Stomach|Other and unspecified parts of tongue|Meninges|Other and unspecified male genital organs|Colon|Connective, subcutaneous and other soft tissues|Bones, joints and articular cartilage of limbs|Ovary|Retroperitoneum and peritoneum|Peripheral nerves and autonomic nervous system|Uterus, NOS|Kidney 259 0
Corpus uteri|Uterus, NOS 538 33
Esophagus|Stomach 184 13
Eye and adnexa 80 0
Heart, mediastinum, and pleura|Bronchus and lung 87 0
Heart, mediastinum, and pleura|Other endocrine glands and related structures|Adrenal gland|Connective, subcutaneous and other soft tissues|Other and ill-defined sites|Spinal cord, cranial nerves, and other parts of central nervous system|Retroperitoneum and peritoneum 179 3
Heart, mediastinum, and pleura|Testis|Stomach|Lymph nodes|Bones, joints and articular cartilage of other and unspecified sites|Brain|Thyroid gland|Small intestine|Colon|Connective, subcutaneous and other soft tissues|Other and unspecified major salivary glands|Retroperitoneum and peritoneum|Hematopoietic and reticuloendothelial systems|Breast 47 0
Heart, mediastinum, and pleura|Thymus 124 2
Kidney 873 130
Liver and intrahepatic bile ducts 372 50
Other and ill-defined sites in lip, oral cavity and pharynx|Palate|Other and unspecified parts of tongue|Hypopharynx|Tonsil|Oropharynx|Larynx|Other and unspecified parts of mouth|Gum|Floor of mouth|Bones, joints and articular cartilage of other and unspecified sites|Lip|Base of tongue 523 44
Other and unspecified parts of biliary tract|Gallbladder|Liver and intrahepatic bile ducts 36 9
Ovary 489 0
Pancreas 178 4
Prostate gland 494 52
Rectosigmoid junction|Colon 444 8
Rectosigmoid junction|Unknown|Rectum|Colon|Connective, subcutaneous and other soft tissues 161 3
Skin 97 2
Stomach 436 41
Testis 150 0
Thyroid gland 506 59
Uterus, NOS 57 0

Let’s consider a following exemplary problem..

We want to find the set of miRNAs the most specific to pancreatic cancer. We see that there are 178 cases of pancreatic cancer miRNA-seq results and only 4 solid tissue normal cases. However, we have multiple normal tissue miRNA-seq results from other projects that could be incorporated in the analysis. Let’s filter and label the samples of interest.

suppressWarnings(suppressMessages(library(dplyr)))

cancer_cases = filter(orginal_TCGA_data, primary_site == "Pancreas" & sample_type == "PrimaryTumor")
control_cases = filter(orginal_TCGA_data, sample_type == "SolidTissueNormal")

The pipeline requires the variable Class with two levels (Cancer and Control) to be present in the dataset.

cancer_cases$Class = "Cancer"
control_cases$Class = "Control"

dataset = rbind(cancer_cases, control_cases)

OmicSelector_table(table(dataset$Class), col.names = c("Class", "Number of cases"))
Class Number of cases
Cancer 178
Control 675
boxplot(dataset$age_at_diagnosis ~ dataset$Class)

t.test(dataset$age_at_diagnosis ~ dataset$Class)
#> 
#>  Welch Two Sample t-test
#> 
#> data:  dataset$age_at_diagnosis by dataset$Class
#> t = 3.88, df = 360.55, p-value = 0.0001242
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>   693.0905 2117.7294
#> sample estimates:
#>  mean in group Cancer mean in group Control 
#>              23782.23              22376.82
OmicSelector_table(table(dataset$gender.x, dataset$Class))
Cancer Control
female 80 334
male 98 325
chisq.test(dataset$gender.x, dataset$Class)
#> 
#>  Pearson's Chi-squared test with Yates' continuity correction
#> 
#> data:  dataset$gender.x and dataset$Class
#> X-squared = 1.6241, df = 1, p-value = 0.2025

There is a stistically significant difference in age between classess. The gender was not associated with class. In order to increase feature selection performance, we will try to balance the sets by performing propensity score matching.

old_dataset = dataset  # backup
dataset = dataset[grepl("Adenocarcinomas", dataset$disease_type), ]
match_by = c("age_at_diagnosis", "gender.x")
tempdane = dplyr::select(dataset, match_by)
tempdane$Class = ifelse(dataset$Class == "Cancer", TRUE, FALSE)
suppressMessages(library(mice))
suppressMessages(library(MatchIt))
temp1 = mice(tempdane, m = 1)
#> 
#>  iter imp variable
#>   1   1  age_at_diagnosis
#>   2   1  age_at_diagnosis
#>   3   1  age_at_diagnosis
#>   4   1  age_at_diagnosis
#>   5   1  age_at_diagnosis
temp2 = temp1$data
temp3 = mice::complete(temp1)
temp3 = temp3[complete.cases(temp3), ]
tempform = OmicSelector_create_formula(match_by)
mod_match <- matchit(tempform, data = temp3)
newdata = match.data(mod_match)
dataset = dataset[as.numeric(rownames(newdata)), ]

Let’s check if there is any imbalance in the new, transformed dataset.

boxplot(dataset$age_at_diagnosis ~ dataset$Class)

t.test(dataset$age_at_diagnosis ~ dataset$Class)
#> 
#>  Welch Two Sample t-test
#> 
#> data:  dataset$age_at_diagnosis by dataset$Class
#> t = 0.090876, df = 351.63, p-value = 0.9276
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>  -827.5374  907.7172
#> sample estimates:
#>  mean in group Cancer mean in group Control 
#>              23782.23              23742.14
OmicSelector_table(table(dataset$gender.x, dataset$Class))
Cancer Control
female 80 79
male 98 99
chisq.test(dataset$gender.x, dataset$Class)
#> 
#>  Pearson's Chi-squared test with Yates' continuity correction
#> 
#> data:  dataset$gender.x and dataset$Class
#> X-squared = 0, df = 1, p-value = 1
fwrite(dataset, "balanced_dataset.csv.gz")

There are no significant differences in age or gender composition between classes now. We can proceed to standard filtering, log-transormation and TPM-normalization.

However, first, in order to stay consistent between different datasets, we need to standardise microRNA names. OmicSelector_correct_miRNA_names() unify the miRNA names between different versions of miRbase.

dataset = OmicSelector_correct_miRNA_names(dataset)  # Correct miRNA names based on the aliases. Useful when analyzing old datasets - to keep the results coherent with current knowledge.
danex = dplyr::select(dataset, starts_with("hsa"))  # Create data.frame or matrix with miRNA counts with miRNAs in columns and cases in rows.
metadane = dplyr::select(dataset, -starts_with("hsa"))  # Metadata with 'Class' variables.
OmicSelector_table(table(metadane$Class))  # Let's be sure that 'Class' variable is correct and contains only 'Cancer' and 'Control' cases.
Var1 Freq
Cancer 178
Control 178
ttpm = OmicSelector_counts_to_log10tpm(danex, metadane, ids = metadane$sample, filtr = T, filtr_minimalcounts = 100, filtr_howmany = 1/3)  # We will leave only the miRNAs which apeared with at least 100 counts in 1/3 of cases.
#> 
#> DGEList unfiltered object with TPM was saved as TPM_DGEList.rds.
#> DGEList filtered object with TPM was saved as TPM_DGEList_filtered.rds.
#> (After filtering) miRNAs left: 166 | filtered out: 2418.
#> Returned data are log10(TPM).

You might have noticed, that we have filtered out microRNAs not having at least 100 counts in 1/3 of samples. It was done to ensure that microRNAs selected as features for classifier (possibly used in clinic) would be detectable in other, cheaper methods, such as qPCR. After filtering there are 166 miRNAs left.

In the next step we will devide the dataset into training, testing and validation datasets. We strongly belive that hold-out validation is the most redundant validation method and although OmicSelector supports cross-validation, the hold-out validation is set by default in most cases. Thus, the rest of the analysis is dependent on existance of 3 seperate datasets:

The best signiture (best set of miRNAs for diagnostic test) can be selected based on all 3 datasets, 2 datasets or only validation set. The process of best signiture selection will be discussed below.

The split can be prepared manually by user (the pipeline expects to find mixed_*.csv files in working directory) or in a convinient way using OmicSelector_prepare_split(). Let’s do it now.

mixed = OmicSelector_prepare_split(metadane = metadane, ttpm = ttpm, train_proc = 0.6)
#> 
#> Saved 3 sets as csv in working directory. Retruned mixed dataset.

Let’s see a split summary.

mixed = fread("mixed.csv")
OmicSelector_table(table(mixed$Class, mixed$mix))
test train valid
Cancer 36 107 35
Control 36 107 35
OmicSelector_table(cbind(mixed[1:10, c(100:105)], Class = mixed[1:10, "Class"]))
hsa-miR-30c-5p hsa-miR-30c-2-3p hsa-miR-30d-5p hsa-miR-139-5p hsa-miR-10a-5p hsa-miR-10b-5p Class.Class
2.598949 1.514444 3.802908 1.555401 4.735516 4.298381 Cancer
2.391663 1.416540 3.656058 1.326116 4.615369 3.946954 Cancer
2.576255 1.566166 3.721311 1.220338 4.385001 3.998914 Cancer
2.260492 1.401010 3.539243 1.924365 3.945605 4.486228 Cancer
2.595315 1.562735 3.571441 1.721510 4.519249 4.126032 Cancer
2.632860 1.723000 3.708020 2.120359 4.875796 3.887056 Cancer
2.747742 2.016887 3.852090 1.533525 3.961177 3.642831 Cancer
3.037578 1.880192 3.960987 1.798007 4.675070 4.133894 Cancer
2.598933 1.291485 3.581714 1.413095 4.580566 3.960672 Cancer
2.829601 1.494520 3.589292 1.755581 4.687104 4.209582 Cancer

We can see that the dataset was devided in balanced way. Now we are ready to move to the analysis…

4 Basic exploratory analysis

In biomarker studies we relay on validation. We perform hold-out validation, so the signature selection has to be based on training dataset only. Including testing and validation dataset in the exploratory analysis could lead to bias (‘data leakage’). In the following section we show how to use our package to perform quick exploratory analysis of miRNA-seq data.

dane = OmicSelector_load_datamix(use_smote_not_rose = T)  # load mixed_*.csv files
train = dane[[1]]
test = dane[[2]]
valid = dane[[3]]
train_smoted = dane[[4]]
trainx = dane[[5]]
trainx_smoted = dane[[6]]  # get the objects from list to make the code more readable.

ks_load_datamix() function loads the data created in preparation phase. It requires the output constructed by OmicSelector_prepare_split() function to be placed in working directory (‘wd’), thus files ‘mixed_train.csv’, ‘mixed_test.csv’ and ‘mixed_valid.csv’ have to exist in the directory. If you have split the data manually, there may be some imbalance of classes in train, test or validation datasets. If so, OmicSelector_prepare_split() perform balancing using:

  1. ROSE (default): https://journal.r-project.org/archive/2014/RJ-2014-008/RJ-2014-008.pdf - by default we generate 10 * number of cases in orginal dataset.
  2. SMOTE: https://arxiv.org/abs/1106.1813 - by defult we use ‘perc.under=100’ and ‘k=10’.

At the beging of the analysis we usually perform principal component analysis (PCA) to assess for any batch effect, possible outliers and get a general understanding of miRNA profile. The package can construct 2-dimentional biplot and 3-dimentional interactive scatterplot based on the computed components.

pca = OmicSelector_PCA(trainx, train$Class)
pca

3D PCA plot may not be shown correctly in Jupyter notebook, but you can check in e.g. R Studio that it worOmicSelector_

pca3d = OmicSelector_PCA_3D(trainx, train$Class)
pca3d

Now we can also correct the batch effect, if there is any. For example, you can use OmicSelector_combat() to do so. However, detailed demonstration is out of scope of this tutorial.

Usually, the next step in the exploratory analysis is to perform the differential expression analysis. Differential expression in our package is biomarker-discovery oriented, thus it uses t-test with the correction for multiple comparisons. The following table shows signifiantly differently expressed miRNAs after Benjamini-Hochberg correction.

de = OmicSelector_differential_expression_ttest(trainx, train$Class)
sig_de = de %>% dplyr::filter(`p-value BH` <= 0.05) %>% dplyr::arrange(`p-value BH`)  # leave only significant after Benjamini-Hochberg procedure and sort by ascending p-value
OmicSelector_table(sig_de)
miR mean logtpm median logtpm SD logtpm cancer mean cancer median cancer SD control mean control median control SD log10FC (subtr estim) log10FC log2FC reversed_log10FC reverse_log2FC p-value p-value Bonferroni p-value Holm -log10(p-value Bonferroni) p-value BH
hsa.miR.21.5p 5.081371 5.120977 0.5409456 5.473043 5.559281 0.3042087 4.689698 4.744446 0.4309906 -0.7833450 0.7833450 2.6022157 0.7833450 2.6022157 0.0000000 0.0000000 0.0000000 32.2312221 0.0000000
hsa.miR.30e.3p 3.654915 3.620465 0.2922656 3.445100 3.469065 0.1835853 3.864731 3.891680 0.2215066 0.4196304 -0.4196304 -1.3939819 -0.4196304 -1.3939819 0.0000000 0.0000000 0.0000000 32.1422635 0.0000000
hsa.miR.30a.3p 3.861758 3.760500 0.5107622 3.494206 3.528067 0.2957390 4.229311 4.315264 0.4049904 0.7351047 -0.7351047 -2.4419651 -0.7351047 -2.4419651 0.0000000 0.0000000 0.0000000 31.8224321 0.0000000
hsa.miR.30c.2.3p 1.791478 1.685323 0.4609305 1.478041 1.473434 0.2548946 2.104915 2.062559 0.4044845 0.6268741 -0.6268741 -2.0824306 -0.6268741 -2.0824306 0.0000000 0.0000000 0.0000000 26.3237118 0.0000000
hsa.miR.132.3p 2.062941 2.061854 0.3206914 2.268277 2.222890 0.2453178 1.857606 1.842071 0.2476985 -0.4106709 0.4106709 1.3642193 0.4106709 1.3642193 0.0000000 0.0000000 0.0000000 23.2892084 0.0000000
hsa.miR.375.3p 3.851381 4.088129 1.1312626 4.572062 4.593208 0.6167635 3.130699 3.420583 1.0689350 -1.4413633 1.4413633 4.7881053 1.4413633 4.7881053 0.0000000 0.0000000 0.0000000 21.6930447 0.0000000
hsa.miR.217.5p 2.065790 1.932856 1.2184284 2.817892 2.596188 1.0079357 1.313689 1.247738 0.9084168 -1.5042026 1.5042026 4.9968529 1.5042026 4.9968529 0.0000000 0.0000000 0.0000000 21.0021448 0.0000000
hsa.miR.139.5p 1.916157 1.919751 0.4638487 1.634747 1.558070 0.3573670 2.197567 2.204857 0.3804627 0.5628209 -0.5628209 -1.8696506 -0.5628209 -1.8696506 0.0000000 0.0000000 0.0000000 20.0671420 0.0000000
hsa.miR.199a.5p 3.034892 3.117770 0.3929526 3.267832 3.318017 0.2924584 2.801951 2.808411 0.3394148 -0.4658802 0.4658802 1.5476204 0.4658802 1.5476204 0.0000000 0.0000000 0.0000000 18.7831163 0.0000000
hsa.miR.338.3p 2.743796 2.778247 0.4190933 2.991348 2.994550 0.3219668 2.496243 2.539407 0.3543332 -0.4951049 0.4951049 1.6447027 0.4951049 1.6447027 0.0000000 0.0000000 0.0000000 18.6530266 0.0000000
hsa.miR.199b.5p 2.146095 2.358829 0.6145137 2.504540 2.573683 0.3567535 1.787650 1.799962 0.6100440 -0.7168901 0.7168901 2.3814574 0.7168901 2.3814574 0.0000000 0.0000000 0.0000000 17.2507100 0.0000000
hsa.miR.127.5p 2.214220 2.327709 0.4803146 2.486170 2.478848 0.3020641 1.942270 1.939357 0.4722596 -0.5438996 0.5438996 1.8067954 0.5438996 1.8067954 0.0000000 0.0000000 0.0000000 16.1634770 0.0000000
hsa.miR.381.3p 1.720930 1.791253 0.4579339 1.974984 1.949285 0.3353016 1.466877 1.476716 0.4226746 -0.5081072 0.5081072 1.6878957 0.5081072 1.6878957 0.0000000 0.0000000 0.0000000 15.6751972 0.0000000
hsa.miR.127.3p 2.789656 2.829601 0.3874414 2.995898 3.006282 0.3147991 2.583413 2.568116 0.3415622 -0.4124850 0.4124850 1.3702456 0.4124850 1.3702456 0.0000000 0.0000000 0.0000000 14.1819049 0.0000000
hsa.miR.199a.3p 3.431280 3.533249 0.3595668 3.620030 3.670480 0.2685999 3.242530 3.285480 0.3401837 -0.3775004 0.3775004 1.2540293 0.3775004 1.2540293 0.0000000 0.0000000 0.0000000 13.5707699 0.0000000
hsa.miR.181b.5p 2.447025 2.523360 0.4131408 2.664941 2.705753 0.2848923 2.229109 2.205351 0.4073655 -0.4358316 0.4358316 1.4478013 0.4358316 1.4478013 0.0000000 0.0000000 0.0000000 13.5990480 0.0000000
hsa.miR.199b.3p 3.430095 3.531945 0.3598114 3.619075 3.669630 0.2686093 3.241115 3.284615 0.3404382 -0.3779599 0.3779599 1.2555557 0.3779599 1.2555557 0.0000000 0.0000000 0.0000000 13.5889555 0.0000000
hsa.miR.194.5p 3.119571 3.359054 0.8329947 3.562675 3.633752 0.4167141 2.676468 2.410622 0.9078933 -0.8862067 0.8862067 2.9439150 0.8862067 2.9439150 0.0000000 0.0000000 0.0000000 13.2390851 0.0000000
hsa.miR.134.5p 2.366486 2.433393 0.4088244 2.572458 2.557931 0.2993653 2.160514 2.115254 0.4007277 -0.4119434 0.4119434 1.3684465 0.4119434 1.3684465 0.0000000 0.0000000 0.0000000 12.1552043 0.0000000
hsa.miR.30a.5p 4.429837 4.356060 0.4519742 4.199892 4.226049 0.2683567 4.659782 4.685628 0.4813796 0.4598896 -0.4598896 -1.5277200 -0.4598896 -1.5277200 0.0000000 0.0000000 0.0000000 12.1052493 0.0000000
hsa.miR.200a.5p 2.480123 2.527551 0.5262405 2.744628 2.777438 0.3622178 2.215619 2.330898 0.5329388 -0.5290086 0.5290086 1.7573286 0.5290086 1.7573286 0.0000000 0.0000000 0.0000000 11.9837197 0.0000000
hsa.miR.136.5p 1.426048 1.539528 0.5852494 1.722033 1.713813 0.2950712 1.130063 1.259715 0.6514071 -0.5919692 0.5919692 1.9664791 0.5919692 1.9664791 0.0000000 0.0000000 0.0000000 11.6576372 0.0000000
hsa.miR.192.5p 3.474000 3.723466 0.8856187 3.920081 3.942126 0.4108526 3.027920 2.831424 1.0027511 -0.8921615 0.8921615 2.9636965 0.8921615 2.9636965 0.0000000 0.0000000 0.0000000 11.4242384 0.0000000
hsa.miR.451a 2.540774 2.525599 0.6339915 2.233131 2.192706 0.4710976 2.848417 2.906464 0.6282318 0.6152860 -0.6152860 -2.0439357 -0.6152860 -2.0439357 0.0000000 0.0000000 0.0000000 11.0384525 0.0000000
hsa.miR.200a.3p 2.330223 2.419049 0.6863313 2.660594 2.674894 0.3970887 1.999851 2.171325 0.7539997 -0.6607432 0.6607432 2.1949415 0.6607432 2.1949415 0.0000000 0.0000000 0.0000000 10.4637303 0.0000000
hsa.miR.141.3p 2.470222 2.587047 0.6758787 2.787653 2.835787 0.4142754 2.152790 2.366831 0.7368061 -0.6348621 0.6348621 2.1089664 0.6348621 2.1089664 0.0000000 0.0000000 0.0000000 9.8966505 0.0000000
hsa.miR.181c.3p 1.549848 1.598609 0.3058360 1.691125 1.690791 0.2009568 1.408572 1.397065 0.3275293 -0.2825529 0.2825529 0.9386203 0.2825529 0.9386203 0.0000000 0.0000000 0.0000000 9.5661290 0.0000000
hsa.miR.30d.5p 3.824938 3.786939 0.2585958 3.705810 3.708020 0.1763818 3.944065 3.950384 0.2731545 0.2382549 -0.2382549 -0.7914657 -0.2382549 -0.7914657 0.0000000 0.0000000 0.0000000 9.5425303 0.0000000
hsa.miR.200b.3p 2.716967 2.769036 0.5121158 2.949316 3.014389 0.3627291 2.484618 2.625241 0.5351976 -0.4646977 0.4646977 1.5436922 0.4646977 1.5436922 0.0000000 0.0000000 0.0000000 9.2128238 0.0000000
hsa.miR.708.3p 1.553047 1.799718 0.7046857 1.878493 1.937453 0.3169286 1.227601 1.186108 0.8267867 -0.6508920 0.6508920 2.1622164 0.6508920 2.1622164 0.0000000 0.0000000 0.0000000 9.1585590 0.0000000
hsa.miR.210.3p 2.239766 2.271507 0.6889295 2.547543 2.542301 0.5385826 1.931988 2.106523 0.6873228 -0.6155552 0.6155552 2.0448301 0.6155552 2.0448301 0.0000000 0.0000000 0.0000000 8.9396288 0.0000000
hsa.miR.486.5p 2.102968 2.062283 0.6191482 1.830616 1.754483 0.4121882 2.375321 2.342782 0.6713086 0.5447046 -0.5447046 -1.8094696 -0.5447046 -1.8094696 0.0000000 0.0000000 0.0000000 8.4375052 0.0000000
hsa.miR.29a.3p 3.841416 3.818064 0.2415932 3.736185 3.745283 0.1796643 3.946646 3.954986 0.2503002 0.2104605 -0.2104605 -0.6991346 -0.2104605 -0.6991346 0.0000000 0.0000000 0.0000000 8.3240291 0.0000000
hsa.miR.378a.3p 2.550650 2.512377 0.3937521 2.378397 2.381114 0.2557418 2.722903 2.778885 0.4315532 0.3445063 -0.3445063 -1.1444252 -0.3445063 -1.1444252 0.0000000 0.0000000 0.0000000 8.2934009 0.0000000
hsa.miR.379.5p 2.828974 2.918613 0.4091041 3.006836 3.034753 0.2966347 2.651112 2.644205 0.4294792 -0.3557240 0.3557240 1.1816895 0.3557240 1.1816895 0.0000000 0.0000000 0.0000000 8.2616630 0.0000000
hsa.miR.141.5p 2.216028 2.392275 0.6525748 2.500775 2.556782 0.3976527 1.931282 2.148570 0.7306892 -0.5694928 0.5694928 1.8918140 0.5694928 1.8918140 0.0000000 0.0000000 0.0000000 8.1778863 0.0000000
hsa.miR.21.3p 2.950511 3.002843 0.4495447 3.143884 3.238660 0.3956108 2.757137 2.698429 0.4172376 -0.3867473 0.3867473 1.2847466 0.3867473 1.2847466 0.0000000 0.0000000 0.0000000 8.1503082 0.0000000
hsa.miR.337.3p 1.498952 1.609902 0.4286748 1.685506 1.704399 0.2599192 1.312398 1.278140 0.4810808 -0.3731072 0.3731072 1.2394354 0.3731072 1.2394354 0.0000000 0.0000000 0.0000000 8.1171714 0.0000000
hsa.miR.144.5p 1.799486 1.840358 0.7365132 1.481479 1.461856 0.4729441 2.117492 2.202314 0.8137450 0.6360122 -0.6360122 -2.1127868 -0.6360122 -2.1127868 0.0000000 0.0000000 0.0000000 8.0043727 0.0000000
hsa.miR.429 1.847904 1.950131 0.7268633 2.162646 2.205144 0.3857231 1.533162 1.702486 0.8443154 -0.6294838 0.6294838 2.0910999 0.6294838 2.0910999 0.0000000 0.0000000 0.0000000 7.8988604 0.0000000
hsa.miR.335.3p 1.773607 1.812886 0.3718545 1.932716 1.892784 0.2426583 1.614497 1.631930 0.4097115 -0.3182195 0.3182195 1.0571023 0.3182195 1.0571023 0.0000000 0.0000000 0.0000000 7.8314098 0.0000000
hsa.miR.126.5p 2.232491 2.222927 0.4152358 2.056938 2.063790 0.2104761 2.408045 2.529680 0.4898455 0.3511067 -0.3511067 -1.1663511 -0.3511067 -1.1663511 0.0000000 0.0000000 0.0000000 7.3936205 0.0000000
hsa.miR.30c.5p 2.808698 2.749100 0.3490929 2.661967 2.661797 0.1963921 2.955429 2.915562 0.4035411 0.2934616 -0.2934616 -0.9748585 -0.2934616 -0.9748585 0.0000000 0.0000000 0.0000000 7.3565035 0.0000000
hsa.miR.181a.3p 2.106380 2.174268 0.3784895 2.261578 2.305816 0.2347854 1.951183 2.028792 0.4290792 -0.3103947 0.3103947 1.0311087 0.3103947 1.0311087 0.0000000 0.0000001 0.0000001 6.9641475 0.0000000
hsa.let.7c.5p 3.419322 3.422382 0.3296842 3.287237 3.332260 0.2860501 3.551407 3.535984 0.3183740 0.2641699 -0.2641699 -0.8775535 -0.2641699 -0.8775535 0.0000000 0.0000002 0.0000001 6.7432319 0.0000000
hsa.miR.181a.5p 3.155295 3.246986 0.4050583 3.316282 3.343112 0.2324404 2.994307 2.991241 0.4725895 -0.3219750 0.3219750 1.0695778 0.3219750 1.0695778 0.0000000 0.0000004 0.0000003 6.3623836 0.0000000
hsa.miR.221.3p 2.290528 2.336670 0.3527519 2.427381 2.408816 0.2861108 2.153674 2.182603 0.3610694 -0.2737072 0.2737072 0.9092357 0.2737072 0.9092357 0.0000000 0.0000007 0.0000005 6.1577028 0.0000000
hsa.miR.93.5p 3.298589 3.328666 0.2589551 3.398683 3.400925 0.1891085 3.198495 3.236571 0.2806412 -0.2001879 0.2001879 0.6650098 0.2001879 0.6650098 0.0000000 0.0000009 0.0000006 6.0433338 0.0000000
hsa.miR.378a.5p 1.765728 1.699123 0.3998851 1.610886 1.612851 0.2430057 1.920570 1.955764 0.4624594 0.3096836 -0.3096836 -1.0287466 -0.3096836 -1.0287466 0.0000000 0.0000011 0.0000008 5.9662895 0.0000000
hsa.miR.146b.5p 2.601785 2.674141 0.4626849 2.779955 2.835954 0.2919913 2.423615 2.450139 0.5299317 -0.3563393 0.3563393 1.1837335 0.3563393 1.1837335 0.0000000 0.0000013 0.0000009 5.8990220 0.0000000
hsa.miR.23a.3p 3.411765 3.464466 0.2170216 3.494149 3.504609 0.1702973 3.329380 3.342163 0.2278979 -0.1647689 0.1647689 0.5473504 0.1647689 0.5473504 0.0000000 0.0000016 0.0000011 5.7880964 0.0000000
hsa.miR.30b.5p 2.622413 2.622930 0.3212403 2.499914 2.507222 0.2120817 2.744913 2.792110 0.3634422 0.2449988 -0.2449988 -0.8138683 -0.2449988 -0.8138683 0.0000000 0.0000017 0.0000012 5.7695073 0.0000000
hsa.miR.625.3p 2.068354 2.104397 0.3502308 2.200772 2.210917 0.2188272 1.935936 1.910435 0.4039743 -0.2648357 0.2648357 0.8797652 0.2648357 0.8797652 0.0000000 0.0000025 0.0000017 5.6075234 0.0000000
hsa.miR.182.5p 3.674023 3.755735 0.4922991 3.858145 3.842168 0.3744427 3.489902 3.616382 0.5275933 -0.3682429 0.3682429 1.2232765 0.3682429 1.2232765 0.0000000 0.0000029 0.0000020 5.5415728 0.0000001
hsa.miR.27a.3p 3.005903 3.044024 0.2647920 3.104509 3.109418 0.2287859 2.907296 2.903005 0.2625226 -0.1972135 0.1972135 0.6551290 0.1972135 0.6551290 0.0000000 0.0000030 0.0000020 5.5228315 0.0000001
hsa.miR.183.5p 3.203446 3.257163 0.4833569 3.381328 3.357706 0.3966813 3.025563 3.143805 0.4982314 -0.3557648 0.3557648 1.1818251 0.3557648 1.1818251 0.0000000 0.0000047 0.0000031 5.3289624 0.0000001
hsa.miR.181c.5p 1.665600 1.682222 0.3601516 1.795267 1.778815 0.2462991 1.535932 1.501756 0.4074728 -0.2593354 0.2593354 0.8614935 0.2593354 0.8614935 0.0000001 0.0000115 0.0000076 4.9383329 0.0000002
hsa.miR.126.3p 3.305734 3.272928 0.4223713 3.157448 3.162873 0.2190488 3.454020 3.630912 0.5158520 0.2965719 -0.2965719 -0.9851906 -0.2965719 -0.9851906 0.0000002 0.0000319 0.0000209 4.4963337 0.0000005
hsa.miR.582.3p 2.087755 2.119436 0.3376004 1.973266 1.974597 0.2964765 2.202245 2.291615 0.3386179 0.2289783 -0.2289783 -0.7606496 -0.2289783 -0.7606496 0.0000004 0.0000584 0.0000380 4.2335770 0.0000010
hsa.miR.143.3p 4.940749 4.860769 0.4133211 4.799815 4.796805 0.2682101 5.081683 4.987285 0.4808783 0.2818686 -0.2818686 -0.9363472 -0.2818686 -0.9363472 0.0000004 0.0000618 0.0000398 4.2090891 0.0000010
hsa.miR.185.5p 1.698820 1.752167 0.3122312 1.803017 1.789962 0.1825995 1.594623 1.585711 0.3750133 -0.2083937 0.2083937 0.6922687 0.2083937 0.6922687 0.0000007 0.0001204 0.0000769 3.9192525 0.0000020
hsa.miR.29c.3p 3.321214 3.327217 0.3591607 3.202955 3.215627 0.2277490 3.439473 3.491354 0.4232090 0.2365180 -0.2365180 -0.7856959 -0.2365180 -0.7856959 0.0000010 0.0001621 0.0001026 3.7900871 0.0000026
hsa.miR.223.3p 2.257390 2.288581 0.4632869 2.408097 2.462940 0.4003810 2.106684 2.111760 0.4744849 -0.3014129 0.3014129 1.0012719 0.3014129 1.0012719 0.0000011 0.0001834 0.0001149 3.7365180 0.0000029
hsa.miR.423.5p 1.545436 1.538957 0.3144486 1.443133 1.425446 0.2069216 1.647738 1.666376 0.3670736 0.2046048 -0.2046048 -0.6796823 -0.2046048 -0.6796823 0.0000013 0.0002154 0.0001337 3.6667565 0.0000034
hsa.miR.151a.5p 1.778564 1.824896 0.2355297 1.854691 1.836098 0.1493639 1.702436 1.739749 0.2783202 -0.1522549 0.1522549 0.5057800 0.1522549 0.5057800 0.0000016 0.0002604 0.0001600 3.5843739 0.0000040
hsa.let.7i.5p 2.599921 2.632392 0.2997045 2.696086 2.717300 0.1738861 2.503755 2.466912 0.3627486 -0.1923305 0.1923305 0.6389080 0.1923305 0.6389080 0.0000020 0.0003296 0.0002005 3.4820413 0.0000050
hsa.miR.26b.5p 2.777405 2.755033 0.2942712 2.683523 2.667076 0.2076405 2.871288 2.871957 0.3363026 0.1877642 -0.1877642 -0.6237392 -0.1877642 -0.6237392 0.0000020 0.0003363 0.0002026 3.4732893 0.0000050
hsa.miR.222.3p 1.679643 1.690400 0.3421027 1.788188 1.797616 0.2933599 1.571098 1.634996 0.3540146 -0.2170897 0.2170897 0.7211563 0.2170897 0.7211563 0.0000021 0.0003468 0.0002068 3.4599760 0.0000051
hsa.miR.320a.3p 2.517259 2.510587 0.2335402 2.443505 2.440882 0.2043264 2.591012 2.575436 0.2384649 0.1475073 -0.1475073 -0.4900086 -0.1475073 -0.4900086 0.0000023 0.0003863 0.0002281 3.4130330 0.0000056
hsa.miR.30e.5p 3.679150 3.640665 0.3123538 3.579560 3.581958 0.1513627 3.778740 3.843580 0.3913006 0.1991799 -0.1991799 -0.6616613 -0.1991799 -0.6616613 0.0000025 0.0004221 0.0002467 3.3745491 0.0000060
hsa.miR.200c.3p 3.479500 3.647500 0.6328315 3.679499 3.713871 0.3714689 3.279502 3.524250 0.7654977 -0.3999973 0.3999973 1.3287624 0.3999973 1.3287624 0.0000028 0.0004717 0.0002728 3.3263079 0.0000066
hsa.miR.145.5p 3.405874 3.362197 0.3557557 3.294171 3.279622 0.2492612 3.517576 3.469948 0.4086525 0.2234046 -0.2234046 -0.7421341 -0.2234046 -0.7421341 0.0000030 0.0004969 0.0002844 3.3037592 0.0000069
hsa.miR.92b.3p 1.748375 1.731752 0.3770581 1.865526 1.808052 0.2617419 1.631225 1.619889 0.4352821 -0.2343014 0.2343014 0.7783325 0.2343014 0.7783325 0.0000039 0.0006400 0.0003624 3.1938498 0.0000088
hsa.miR.629.5p 1.718671 1.767577 0.2822432 1.804344 1.819456 0.2016194 1.632997 1.650836 0.3234272 -0.1713470 0.1713470 0.5692024 0.1713470 0.5692024 0.0000064 0.0010697 0.0005993 2.9707322 0.0000145
hsa.miR.99a.5p 2.916024 2.912899 0.3862114 2.800660 2.801168 0.3181101 3.031388 3.020665 0.4143220 0.2307282 -0.2307282 -0.7664624 -0.2307282 -0.7664624 0.0000086 0.0014262 0.0007904 2.8458122 0.0000190
hsa.miR.22.3p 4.901288 4.935034 0.2599745 4.979132 4.983023 0.1344526 4.823443 4.825832 0.3248074 -0.1556883 0.1556883 0.5171853 0.1556883 0.5171853 0.0000101 0.0016706 0.0009158 2.7771206 0.0000220
hsa.miR.10b.5p 4.284825 4.160990 0.6577961 4.092498 4.126032 0.2208435 4.477153 4.339191 0.8637267 0.3846552 -0.3846552 -1.2777969 -0.3846552 -1.2777969 0.0000184 0.0030501 0.0016537 2.5156825 0.0000396
hsa.miR.142.3p 2.908082 2.993345 0.5523317 3.062898 3.069081 0.3324835 2.753266 2.754739 0.6738583 -0.3096321 0.3096321 1.0285755 0.3096321 1.0285755 0.0000350 0.0058148 0.0031176 2.2354673 0.0000745
hsa.miR.16.5p 2.418426 2.396977 0.2678058 2.344887 2.354009 0.1520643 2.491965 2.532161 0.3317754 0.1470782 -0.1470782 -0.4885833 -0.1470782 -0.4885833 0.0000518 0.0086050 0.0045617 2.0652508 0.0001089
hsa.miR.10a.5p 4.453193 4.572159 0.4172756 4.567356 4.619375 0.2726925 4.339031 4.448143 0.4992066 -0.2283251 0.2283251 0.7584795 0.2283251 0.7584795 0.0000528 0.0087721 0.0045974 2.0568959 0.0001097
hsa.miR.365a.3p 1.558982 1.524607 0.3288053 1.472455 1.482687 0.2603646 1.645509 1.646930 0.3665257 0.1730535 -0.1730535 -0.5748714 -0.1730535 -0.5748714 0.0000972 0.0161318 0.0083574 1.7923179 0.0001970
hsa.miR.365b.3p 1.559072 1.524607 0.3286232 1.472600 1.482687 0.2598729 1.645545 1.646930 0.3665720 0.1729456 -0.1729456 -0.5745130 -0.1729456 -0.5745130 0.0000973 0.0161562 0.0083574 1.7916615 0.0001970
hsa.miR.20a.5p 2.167170 2.188072 0.3531756 2.258504 2.252491 0.2151305 2.075836 2.092815 0.4330362 -0.1826683 0.1826683 0.6068109 0.1826683 0.6068109 0.0001387 0.0230266 0.0116520 1.6377698 0.0002774
hsa.miR.195.5p 1.610326 1.644712 0.4593292 1.492892 1.530241 0.2351047 1.727760 1.829698 0.5838159 0.2348685 -0.2348685 -0.7802161 -0.2348685 -0.7802161 0.0001727 0.0286635 0.0143318 1.5426701 0.0003412
hsa.miR.26a.5p 3.363368 3.336961 0.2249507 3.307628 3.297116 0.1471895 3.419108 3.407502 0.2715615 0.1114806 -0.1114806 -0.3703306 -0.1114806 -0.3703306 0.0002606 0.0432635 0.0213711 1.3638783 0.0005090
hsa.miR.145.3p 1.779374 1.754841 0.2975307 1.706504 1.693139 0.2239980 1.852244 1.840403 0.3420364 0.1457395 -0.1457395 -0.4841363 -0.1457395 -0.4841363 0.0002988 0.0495960 0.0242005 1.3045533 0.0005767
hsa.miR.142.5p 1.517108 1.642632 0.7709832 1.707036 1.728336 0.3336782 1.327180 1.413437 1.0051222 -0.3798562 0.3798562 1.2618548 0.3798562 1.2618548 0.0003066 0.0509030 0.0245316 1.2932569 0.0005851
hsa.miR.155.5p 2.133480 2.195366 0.4195203 2.233687 2.297068 0.3475670 2.033272 2.006969 0.4610634 -0.2004154 0.2004154 0.6657657 0.2004154 0.6657657 0.0004167 0.0691679 0.0329172 1.1600957 0.0007860
hsa.let.7d.5p 2.204108 2.185887 0.2122742 2.154807 2.147458 0.1420691 2.253409 2.269843 0.2558420 0.0986016 -0.0986016 -0.3275473 -0.0986016 -0.3275473 0.0006292 0.1044446 0.0490764 0.9811142 0.0011735
hsa.miR.101.3p 4.064812 4.041831 0.3932389 3.975163 3.934040 0.1680979 4.154461 4.258030 0.5159943 0.1792983 -0.1792983 -0.5956161 -0.1792983 -0.5956161 0.0008471 0.1406149 0.0652250 0.8519688 0.0015624
hsa.miR.15a.5p 1.962872 1.985385 0.2869339 2.027709 2.007988 0.1768348 1.898034 1.940992 0.3545154 -0.1296752 0.1296752 0.4307717 0.1296752 0.4307717 0.0008984 0.1491266 0.0678151 0.8264448 0.0016209
hsa.miR.140.3p 3.000561 3.018035 0.2271711 2.949429 2.935298 0.2005767 3.051693 3.090265 0.2412282 0.1022638 -0.1022638 -0.3397129 -0.1022638 -0.3397129 0.0008923 0.1481224 0.0678151 0.8293794 0.0016209
hsa.miR.193a.5p 2.336431 2.300347 0.3276854 2.266929 2.278125 0.1938504 2.405932 2.378371 0.4104126 0.1390021 -0.1390021 -0.4617551 -0.1390021 -0.4617551 0.0018588 0.3085666 0.1375538 0.5106511 0.0033179
hsa.let.7b.5p 4.195831 4.209035 0.2924159 4.256938 4.282751 0.1889508 4.134724 4.104211 0.3585804 -0.1222138 0.1222138 0.4059855 0.1222138 0.4059855 0.0021512 0.3570954 0.1570359 0.4472157 0.0037989
hsa.miR.425.5p 1.923042 1.930834 0.3243793 1.987356 1.978949 0.2395357 1.858729 1.880977 0.3817182 -0.1286263 0.1286263 0.4272874 0.1286263 0.4272874 0.0035774 0.5938450 0.2575713 0.2263269 0.0062510
hsa.miR.99b.5p 4.315202 4.300285 0.2601134 4.263737 4.282048 0.1951765 4.366667 4.343604 0.3041630 0.1029303 -0.1029303 -0.3419271 -0.1029303 -0.3419271 0.0036421 0.6045962 0.2585923 0.2185346 0.0062979
hsa.miR.146b.3p 1.886946 1.965307 0.4754291 1.979342 1.993235 0.3044790 1.794549 1.860622 0.5867326 -0.1847929 0.1847929 0.6138687 0.1847929 0.6138687 0.0043674 0.7249845 0.3057163 0.1396713 0.0074741
hsa.miR.128.3p 1.955925 1.943604 0.2304255 2.000480 1.993252 0.1994596 1.911370 1.897153 0.2508004 -0.0891101 0.0891101 0.2960174 0.0891101 0.2960174 0.0044531 0.7392212 0.3072666 0.1312256 0.0075431
hsa.miR.34a.5p 2.074666 2.121651 0.2675331 2.125712 2.136585 0.1931050 2.023620 2.059319 0.3182343 -0.1020923 0.1020923 0.3391431 0.1020923 0.3391431 0.0050922 0.8453067 0.3462702 0.0729857 0.0085385
hsa.miR.1307.5p 2.032668 2.074195 0.4746939 2.121558 2.143052 0.3137240 1.943777 1.930948 0.5817384 -0.1777808 0.1777808 0.5905749 0.1777808 0.5905749 0.0060341 1.0000000 0.4042856 0.0000000 0.0100166
hsa.miR.146a.5p 1.834930 1.878293 0.5428638 1.936147 1.968467 0.3763981 1.733712 1.804289 0.6556095 -0.2024345 0.2024345 0.6724729 0.2024345 0.6724729 0.0062340 1.0000000 0.4114442 0.0000000 0.0102460
hsa.miR.660.5p 1.637156 1.706445 0.5648980 1.742335 1.736172 0.1929619 1.531977 1.656099 0.7626676 -0.2103579 0.2103579 0.6987938 0.2103579 0.6987938 0.0065781 1.0000000 0.4275745 0.0000000 0.0107055
hsa.miR.1307.3p 2.668366 2.682073 0.3103661 2.725068 2.712113 0.1957961 2.611663 2.652759 0.3856627 -0.1134058 0.1134058 0.3767259 0.1134058 0.3767259 0.0074280 1.0000000 0.4753900 0.0000000 0.0119713
hsa.miR.17.3p 2.280466 2.310070 0.2760079 2.330198 2.324300 0.1630184 2.230733 2.251456 0.3485844 -0.0994646 0.0994646 0.3304142 0.0994646 0.3304142 0.0083333 1.0000000 0.5249975 0.0000000 0.0133012
hsa.miR.103a.3p 4.078473 4.104653 0.2058716 4.115271 4.122395 0.1680536 4.041675 4.049734 0.2327882 -0.0735962 0.0735962 0.2444812 0.0735962 0.2444812 0.0086789 1.0000000 0.5380907 0.0000000 0.0137209
hsa.miR.484 1.597652 1.580193 0.2719205 1.550795 1.553409 0.1598979 1.644510 1.656175 0.3443530 0.0937157 -0.0937157 -0.3113168 -0.0937157 -0.3113168 0.0116710 1.0000000 0.7119329 0.0000000 0.0182773
hsa.miR.452.5p 1.609759 1.684291 0.4772755 1.691423 1.719895 0.2895699 1.528095 1.619481 0.6003483 -0.1633282 0.1633282 0.5425647 0.1633282 0.5425647 0.0122598 1.0000000 0.7355852 0.0000000 0.0189271
hsa.miR.584.5p 1.562512 1.609699 0.4055066 1.631695 1.617142 0.3258710 1.493330 1.570896 0.4632148 -0.1383646 0.1383646 0.4596372 0.1383646 0.4596372 0.0123140 1.0000000 0.7355852 0.0000000 0.0189271
hsa.miR.9.5p 2.452682 2.417320 0.5298502 2.364790 2.362214 0.3600516 2.540574 2.612118 0.6472233 0.1757844 -0.1757844 -0.5839430 -0.1757844 -0.5839430 0.0151165 1.0000000 0.8767577 0.0000000 0.0230215
hsa.miR.361.3p 2.114070 2.138671 0.2668813 2.157051 2.182644 0.1719882 2.071090 2.091288 0.3313815 -0.0859613 0.0859613 0.2855574 0.0859613 0.2855574 0.0184170 1.0000000 1.0000000 0.0000000 0.0277930
hsa.let.7g.5p 2.743360 2.731598 0.2633678 2.701240 2.687710 0.2007329 2.785480 2.824734 0.3090374 0.0842401 -0.0842401 -0.2798397 -0.0842401 -0.2798397 0.0191012 1.0000000 1.0000000 0.0000000 0.0285658
hsa.let.7a.3p 1.362918 1.456311 0.5840349 1.454096 1.472496 0.2172292 1.271740 1.413722 0.7883141 -0.1823566 0.1823566 0.6057754 0.1823566 0.6057754 0.0227488 1.0000000 1.0000000 0.0000000 0.0337170
hsa.miR.28.3p 3.478699 3.452430 0.2371295 3.442283 3.445475 0.2164372 3.515115 3.488616 0.2519303 0.0728325 -0.0728325 -0.2419443 -0.0728325 -0.2419443 0.0243409 1.0000000 1.0000000 0.0000000 0.0355939
hsa.miR.23b.3p 3.145549 3.139008 0.1654088 3.120156 3.106189 0.1396735 3.170942 3.185124 0.1848453 0.0507862 -0.0507862 -0.1687082 -0.0507862 -0.1687082 0.0244440 1.0000000 1.0000000 0.0000000 0.0355939
hsa.miR.29b.3p 2.730065 2.739194 0.3702233 2.785646 2.771371 0.2357865 2.674484 2.713670 0.4621597 -0.1111620 0.1111620 0.3692721 0.1111620 0.3692721 0.0281053 1.0000000 1.0000000 0.0000000 0.0405694

Let’s visualize the results of differential expression using heatmap and vulcano plot.

OmicSelector_heatmap(x = dplyr::select(trainx, sig_de$miR), rlab = data.frame(Class = train$Class), zscore = F, margins = c(10, 10))

Z-scoring the values before clustering and plotting will help us to gain more insight.

OmicSelector_heatmap(x = dplyr::select(trainx, sig_de$miR), rlab = data.frame(Class = train$Class), zscore = T, margins = c(10, 10))

We will also create a vulcano plot and label top 10 most significant miRNAs:

OmicSelector_vulcano_plot(selected_miRNAs = de$miR, DE = de, only_label = sig_de$miR[1:10])

We may also what to check the consistency of differential expression between datasets:

de_test = OmicSelector_differential_expression_ttest(dplyr::select(test, starts_with("hsa")), test$Class)
de_valid = OmicSelector_differential_expression_ttest(dplyr::select(valid, starts_with("hsa")), valid$Class)
OmicSelector_correlation_plot(de$log2FC, de_test$log2FC, "log2FC on training set", "log2FC on test set", "", yx = T)

OmicSelector_correlation_plot(de$log2FC, de_valid$log2FC, "log2FC on training set", "log2FC on validation set", "", yx = T)

OmicSelector_correlation_plot(de_test$log2FC, de_valid$log2FC, "log2FC on test set", "log2FC on validation set", "", yx = T)

5 miRNA selection

The main feature of this package is the shotgun-like feature selection evaluation of possible miRNA signatures of biological processes. The function can be applied in a straightforward way, e.g.:

selected_features = OmicSelector_OmicSelector(wd = getwd(), m = 1:10, max_iterations = 1, stamp = "tutorial")  # we just run only first 10 methods for the sake of speed.

But, for largers projects we suggest using the following wrapper wich will perform the feature selection in parallel, significantly reducing computational time. We do not recommend using more than 5 threads, beacuse some of the methods inhereditly use multicore processing:

readLines("Tutorial_OmicSelector.R") %>% paste0(collapse = "\n") %>% cat
#> #options(warn = -1)
#> suppressMessages(library(foreach))
#> suppressMessages(library(doParallel))
#> suppressMessages(library(parallel))
#> suppressMessages(library(doParallel))
#> 
#> m = 1:56 # which methods to check?
#> 
#> cl <- makePSOCKcluster(useXDR = TRUE, 5) # We do not recommend using more than 5 threads, beacuse some of the methods inhereditly use multicore processing.
#> doParallel:: registerDoParallel(cl)
#> iterations = length(m)
#> pb <- txtProgressBar(max = iterations, style = 3)
#> progress <- function(n) setTxtProgressBar(pb, n)
#> opts <- list(progress = progress)
#> foreach(i = m, .options.snow = opts) %dopar%
#> {
#>   suppressMessages(library(OmicSelector))
#>   # setwd("/OmicSelector/OmicSelector/vignettes") # change it you to your working directory
#>   OmicSelector_OmicSelector(m = i, max_iterations = 1, stamp = "tutorial", debug = F, # we set debug to false (to make the package smaller), you may also want to change stamp to something meaningful, max_iterations was set to 1 to recude the computational time.. in real life scenarios it is resonable to use at least 10 iterations.
#>                   prefer_no_features = 11, # Few methods are filter rather than wrapper methods, thus requires the maximum number of maximum features.
#>                   conda_path = "/opt/conda/bin/conda", # Methods line WxNet requires usage of python. In setup script we create conda enviorment. Providing conda_path makes it easier to activate env. We prefer this apporach over use_condaenv.
#>                   timeout = 600) # We don't want to wait eternity in this tutorial, just 10 minutes. Timeout is useful for complicated methods. Depending on your CPU 2 days may be reasonable for larger projects. Note that some methods cannot be controled with timeout parameter.
#> }
#> 
#> stopCluster(cl)
#> #options(warn = 0)

If you are using our enviorment to learn this package you can tweak and run this code in the interactive notebook. Click here.

A few notes about what is does:

Files created for each method (e.g. for stamp=tutorial and m=1):

Pearls about the methods:

Notes about methods:

Comming soon…

The OmicSelector functions saves all output files to temp/ directory. As users may want to run multiple selection methods in different configurations, we do not recommend using the return of this function in the following steps. Instead, we provide OmicSelector_merge_formulas() which conviniently summerizes the results of feature selection. We can do:

selected_sets_of_miRNAs = OmicSelector_merge_formulas(max_miRNAs = 11)  # we filter out sets with more than 11 miRNAs.
selected_sets_of_miRNAs_with_own = OmicSelector_merge_formulas(max_miRNAs = 11, add = list(my_own_signature = c("hsa.miR.192.5p", "hsa.let.7g.5p", "hsa.let.7a.5p", 
    "hsa.let.7d.5p", "hsa.miR.194.5p", "hsa.miR.98.5p", "hsa.let.7f.5p", "hsa.miR.26b.5p")))  # you can also add your own signature (for example selected from literature)

Note that:

Let’s analyze the process of feature selection:

all_sets = readRDS("featureselection_formulas_all.RDS")
length(all_sets)  # How many feature selection methods completed in time?
#> [1] 23
final_sets = readRDS("featureselection_formulas_final.RDS")
length(final_sets)  # How many feature selection methods completed in time and fulfilled max_miRNA criteria? (remember about fcsig and cfs_sig)
#> [1] 14
featureselection_formulas_final = fread("featureselection_formulas_final.csv")
OmicSelector_table(featureselection_formulas_final)  # show information about selected formulas
name formula ile_miRNA
cfs_sig Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p 34
fcsig Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p 50
my_own_signature Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p 0
sigtop Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 11
sigtopBonf Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 11
sigtopHolm Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 11
topFC Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p 11
sigtopSMOTE Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 11
sigtopBonfSMOTE Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 11
sigtopHolmSMOTE Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 11
topFCSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p 11
cfsSMOTE Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p 5
cfsSMOTE_sig Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p 5
fcfsSMOTE Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.708.3p + hsa.miR.375.3p + hsa.miR.30e.3p 5

Note that my_own_signture has 0 miRNAs according to the table. This trick is done to make sure that signatures added manually will not be filtered out based on max_miRNA parameter.

Now, we will summarize number of microRNAs selected by methods implemented in OmicSelector_OmicSelector by creating histogram and calculating some descriptive statistics.

hist(featureselection_formulas_final$ile_miRNA[-which(featureselection_formulas_final$ile_miRNA == 0)], breaks = ncol(train), main = "Number of selected microRNAs distribution", 
    xlab = "Number of selected microRNAs")  # Histogram showing how many miRNAs were selected in final set.

psych::describe(featureselection_formulas_final$ile_miRNA[-which(featureselection_formulas_final$ile_miRNA == 0)])  # Descriptive statistics of how many features where selected in the final set.
#>    vars  n  mean    sd median trimmed mad min max range skew kurtosis   se
#> X1    1 13 14.38 12.94     11      12   0   5  50    45 1.77     1.89 3.59

6 Benchmarking

In the next step of looking for the best microRNA signature, we perform benchmarking. This tests all the signatures using different classifier architectures. Here is the example of benchmark with default parameters:

readLines("Tutorial_benchmark.R") %>% paste0(collapse = "\n") %>% cat

If you are using our enviorment to learn this package you can tweak and run this code in the interactive notebook. Click here.

Just for rendering this tutorial we will use a very simple benchmark using only logistic regression and conditional trees.

OmicSelector_benchmark(search_iters = 5, # 5 random hyperparameter sets will be checked; 5 is set here for speed purposes.. for real projects use more, like 5000...
            algorithms = c("ctree"), # just add ctree, note that logistic regression (glm) is always included
            output_file = paste0("benchmark.csv")) # the main output
#>              method SMOTE
#> 1           cfs_sig    No
#> 2             fcsig    No
#> 3  my_own_signature    No
#> 4            sigtop    No
#> 5        sigtopBonf    No
#> 6        sigtopHolm    No
#> 7             topFC    No
#> 8       sigtopSMOTE   Yes
#> 9   sigtopBonfSMOTE   Yes
#> 10  sigtopHolmSMOTE   Yes
#> 11       topFCSMOTE   Yes
#> 12         cfsSMOTE   Yes
#> 13     cfsSMOTE_sig   Yes
#> 14        fcfsSMOTE   Yes
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      miRy
#> 1                                                                                                                                                                                                                                                                                       Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + \n    hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p
#> 2  Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + \n    hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p
#> 3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p
#> 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 7                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
#> 8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
#> 12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p
#> 13                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p
#> 14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.708.3p + hsa.miR.375.3p + hsa.miR.30e.3p
#>    glm_modelname glm_train_ROCAUC glm_train_ROCAUC_lower95CI
#> 1     1589408746        1.0000000                          1
#> 2     1589408757        1.0000000                          1
#> 3     1589408768        0.9239235          0.890138639558989
#> 4     1589408779        0.9961569          0.990219096927101
#> 5     1589408789        0.9961569          0.990219096927101
#> 6     1589408800        0.9961569          0.990219096927101
#> 7     1589408810        0.9939733          0.985662071431939
#> 8     1589408820        0.9954188          0.994886530432955
#> 9     1589408845        0.9954188          0.994886530432955
#> 10    1589408870        0.9954188          0.994886530432955
#> 11    1589408897        0.9977293          0.997300123062692
#> 12    1589408921        0.9971039          0.996457027614093
#> 13    1589408941        0.9971039          0.996457027614093
#> 14    1589408964        0.9971039          0.996457027614093
#>    glm_train_ROCAUC_upper95CI glm_train_Accuracy glm_train_Sensitivity
#> 1                           1          1.0000000             1.0000000
#> 2                           1          1.0000000             1.0000000
#> 3           0.957708333975817          0.8317757             0.8504673
#> 4                           1          0.9859813             1.0000000
#> 5                           1          0.9859813             1.0000000
#> 6                           1          0.9859813             1.0000000
#> 7                           1          0.9813084             0.9906542
#> 8           0.995951097307459          0.9748454             0.9731776
#> 9           0.995951097307459          0.9748454             0.9731776
#> 10          0.995951097307459          0.9748454             0.9731776
#> 11          0.998158531720596          0.9912587             1.0000000
#> 12          0.997750828318674          0.9839587             0.9811215
#> 13          0.997750828318674          0.9839587             0.9811215
#> 14          0.997750828318674          0.9839587             0.9811215
#>    glm_train_Specificity glm_test_Accuracy glm_test_Sensitivity
#> 1              1.0000000         0.8888889            0.9166667
#> 2              1.0000000         0.9166667            0.9166667
#> 3              0.8130841         0.8472222            0.8055556
#> 4              0.9719626         0.9444444            1.0000000
#> 5              0.9719626         0.9444444            1.0000000
#> 6              0.9719626         0.9444444            1.0000000
#> 7              0.9719626         0.9444444            1.0000000
#> 8              0.9764967         0.8888889            0.9166667
#> 9              0.9764967         0.8888889            0.9166667
#> 10             0.9764967         0.8888889            0.9166667
#> 11             0.9826039         0.9444444            1.0000000
#> 12             0.9867678         0.9305556            0.9722222
#> 13             0.9867678         0.9305556            0.9722222
#> 14             0.9867678         0.9305556            0.9722222
#>    glm_test_Specificity glm_valid_Accuracy glm_valid_Sensitivity
#> 1             0.8611111          1.0000000             1.0000000
#> 2             0.9166667          0.9571429             1.0000000
#> 3             0.8888889          0.8857143             0.8857143
#> 4             0.8888889          0.9714286             1.0000000
#> 5             0.8888889          0.9714286             1.0000000
#> 6             0.8888889          0.9714286             1.0000000
#> 7             0.8888889          0.9857143             1.0000000
#> 8             0.8611111          0.9714286             1.0000000
#> 9             0.8611111          0.9714286             1.0000000
#> 10            0.8611111          0.9714286             1.0000000
#> 11            0.8888889          0.9857143             1.0000000
#> 12            0.8888889          0.9857143             1.0000000
#> 13            0.8888889          0.9857143             1.0000000
#> 14            0.8888889          0.9857143             1.0000000
#>    glm_valid_Specificity ctree_modelname ctree_train_ROCAUC
#> 1              1.0000000      1589409024          0.9768539
#> 2              0.9142857      1589409035          0.9943663
#> 3              0.8857143      1589409047          0.9753254
#> 4              0.9428571      1589409058          0.9905232
#> 5              0.9428571      1589409070          0.9905232
#> 6              0.9428571      1589409082          0.9905232
#> 7              0.9714286      1589409093          0.9944537
#> 8              0.9428571      1589409105          0.9999357
#> 9              0.9428571      1589409129          0.9999357
#> 10             0.9428571      1589409151          0.9999357
#> 11             0.9714286      1589409176          0.9999653
#> 12             0.9714286      1589409197          0.9995422
#> 13             0.9714286      1589409218          0.9995422
#> 14             0.9714286      1589409238          0.9995422
#>    ctree_train_ROCAUC_lower95CI ctree_train_ROCAUC_upper95CI
#> 1             0.956749862266401            0.996957885135119
#> 2             0.989250362911224            0.999482277494052
#> 3             0.960566402099731            0.990084309752833
#> 4             0.979470550029621                            1
#> 5             0.979470550029621                            1
#> 6             0.979470550029621                            1
#> 7             0.989338017532758            0.999569310618172
#> 8             0.999845878128999                            1
#> 9             0.999845878128999                            1
#> 10            0.999845878128999                            1
#> 11            0.999902047822822                            1
#> 12            0.999363841491172            0.999720535284351
#> 13            0.999363841491172            0.999720535284351
#> 14            0.999363841491172            0.999720535284351
#>    ctree_train_Accuracy ctree_train_Sensitivity ctree_train_Specificity
#> 1             0.9485981               0.9813084               0.9158879
#> 2             0.9579439               0.9345794               0.9813084
#> 3             0.8971963               0.8317757               0.9626168
#> 4             0.9579439               0.9345794               0.9813084
#> 5             0.9579439               0.9345794               0.9813084
#> 6             0.9579439               0.9345794               0.9813084
#> 7             0.9579439               0.9906542               0.9252336
#> 8             0.9993955               1.0000000               0.9987971
#> 9             0.9993955               1.0000000               0.9987971
#> 10            0.9993955               1.0000000               0.9987971
#> 11            0.9996745               1.0000000               0.9993523
#> 12            0.9981866               1.0000000               0.9963912
#> 13            0.9981866               1.0000000               0.9963912
#> 14            0.9981866               1.0000000               0.9963912
#>    ctree_test_Accuracy ctree_test_Sensitivity ctree_test_Specificity
#> 1            0.9305556              1.0000000              0.8611111
#> 2            0.9166667              0.9444444              0.8888889
#> 3            0.7916667              0.6944444              0.8888889
#> 4            0.9166667              0.9444444              0.8888889
#> 5            0.9166667              0.9444444              0.8888889
#> 6            0.9166667              0.9444444              0.8888889
#> 7            0.9305556              0.9722222              0.8888889
#> 8            0.8611111              0.7500000              0.9722222
#> 9            0.8611111              0.7500000              0.9722222
#> 10           0.8611111              0.7500000              0.9722222
#> 11           0.9444444              0.8888889              1.0000000
#> 12           0.9444444              0.9444444              0.9444444
#> 13           0.9444444              0.9444444              0.9444444
#> 14           0.9444444              0.9444444              0.9444444
#>    ctree_valid_Accuracy ctree_valid_Sensitivity ctree_valid_Specificity
#> 1             0.9571429               1.0000000               0.9142857
#> 2             0.9571429               0.9714286               0.9428571
#> 3             0.8714286               0.8000000               0.9428571
#> 4             0.9571429               0.9714286               0.9428571
#> 5             0.9571429               0.9714286               0.9428571
#> 6             0.9571429               0.9714286               0.9428571
#> 7             0.9714286               1.0000000               0.9428571
#> 8             0.9428571               0.8857143               1.0000000
#> 9             0.9428571               0.8857143               1.0000000
#> 10            0.9428571               0.8857143               1.0000000
#> 11            0.9571429               0.9142857               1.0000000
#> 12            0.9571429               0.9428571               0.9714286
#> 13            0.9571429               0.9428571               0.9714286
#> 14            0.9571429               0.9428571               0.9714286

As benchmarking is done, the main result file is saved in file specified in output_file parameter. It contains the performance metrics of signatures satisfying initial criteria (e.g. max_miRNA) across different methods of modelling. Let’s take a quick look:

OmicSelector_table(fread("benchmark.csv"))
V1 method SMOTE miRy glm_modelname glm_train_ROCAUC glm_train_ROCAUC_lower95CI glm_train_ROCAUC_upper95CI glm_train_Accuracy glm_train_Sensitivity glm_train_Specificity glm_test_Accuracy glm_test_Sensitivity glm_test_Specificity glm_valid_Accuracy glm_valid_Sensitivity glm_valid_Specificity ctree_modelname ctree_train_ROCAUC ctree_train_ROCAUC_lower95CI ctree_train_ROCAUC_upper95CI ctree_train_Accuracy ctree_train_Sensitivity ctree_train_Specificity ctree_test_Accuracy ctree_test_Sensitivity ctree_test_Specificity ctree_valid_Accuracy ctree_valid_Sensitivity ctree_valid_Specificity
1 cfs_sig No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p 1589408746 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.8888889 0.9166667 0.8611111 1.0000000 1.0000000 1.0000000 1589409024 0.9768539 0.9567499 0.9969579 0.9485981 0.9813084 0.9158879 0.9305556 1.0000000 0.8611111 0.9571429 1.0000000 0.9142857
2 fcsig No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p 1589408757 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9166667 0.9166667 0.9166667 0.9571429 1.0000000 0.9142857 1589409035 0.9943663 0.9892504 0.9994823 0.9579439 0.9345794 0.9813084 0.9166667 0.9444444 0.8888889 0.9571429 0.9714286 0.9428571
3 my_own_signature No Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p 1589408768 0.9239235 0.8901386 0.9577083 0.8317757 0.8504673 0.8130841 0.8472222 0.8055556 0.8888889 0.8857143 0.8857143 0.8857143 1589409047 0.9753254 0.9605664 0.9900843 0.8971963 0.8317757 0.9626168 0.7916667 0.6944444 0.8888889 0.8714286 0.8000000 0.9428571
4 sigtop No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 1589408779 0.9961569 0.9902191 1.0000000 0.9859813 1.0000000 0.9719626 0.9444444 1.0000000 0.8888889 0.9714286 1.0000000 0.9428571 1589409058 0.9905232 0.9794706 1.0000000 0.9579439 0.9345794 0.9813084 0.9166667 0.9444444 0.8888889 0.9571429 0.9714286 0.9428571
5 sigtopBonf No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 1589408789 0.9961569 0.9902191 1.0000000 0.9859813 1.0000000 0.9719626 0.9444444 1.0000000 0.8888889 0.9714286 1.0000000 0.9428571 1589409070 0.9905232 0.9794706 1.0000000 0.9579439 0.9345794 0.9813084 0.9166667 0.9444444 0.8888889 0.9571429 0.9714286 0.9428571
6 sigtopHolm No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p 1589408800 0.9961569 0.9902191 1.0000000 0.9859813 1.0000000 0.9719626 0.9444444 1.0000000 0.8888889 0.9714286 1.0000000 0.9428571 1589409082 0.9905232 0.9794706 1.0000000 0.9579439 0.9345794 0.9813084 0.9166667 0.9444444 0.8888889 0.9571429 0.9714286 0.9428571
7 topFC No Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p 1589408810 0.9939733 0.9856621 1.0000000 0.9813084 0.9906542 0.9719626 0.9444444 1.0000000 0.8888889 0.9857143 1.0000000 0.9714286 1589409093 0.9944537 0.9893380 0.9995693 0.9579439 0.9906542 0.9252336 0.9305556 0.9722222 0.8888889 0.9714286 1.0000000 0.9428571
8 sigtopSMOTE Yes Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 1589408820 0.9954188 0.9948865 0.9959511 0.9748454 0.9731776 0.9764967 0.8888889 0.9166667 0.8611111 0.9714286 1.0000000 0.9428571 1589409105 0.9999357 0.9998459 1.0000000 0.9993955 1.0000000 0.9987971 0.8611111 0.7500000 0.9722222 0.9428571 0.8857143 1.0000000
9 sigtopBonfSMOTE Yes Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 1589408845 0.9954188 0.9948865 0.9959511 0.9748454 0.9731776 0.9764967 0.8888889 0.9166667 0.8611111 0.9714286 1.0000000 0.9428571 1589409129 0.9999357 0.9998459 1.0000000 0.9993955 1.0000000 0.9987971 0.8611111 0.7500000 0.9722222 0.9428571 0.8857143 1.0000000
10 sigtopHolmSMOTE Yes Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p 1589408870 0.9954188 0.9948865 0.9959511 0.9748454 0.9731776 0.9764967 0.8888889 0.9166667 0.8611111 0.9714286 1.0000000 0.9428571 1589409151 0.9999357 0.9998459 1.0000000 0.9993955 1.0000000 0.9987971 0.8611111 0.7500000 0.9722222 0.9428571 0.8857143 1.0000000
11 topFCSMOTE Yes Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p 1589408897 0.9977293 0.9973001 0.9981585 0.9912587 1.0000000 0.9826039 0.9444444 1.0000000 0.8888889 0.9857143 1.0000000 0.9714286 1589409176 0.9999653 0.9999020 1.0000000 0.9996745 1.0000000 0.9993523 0.9444444 0.8888889 1.0000000 0.9571429 0.9142857 1.0000000
12 cfsSMOTE Yes Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p 1589408921 0.9971039 0.9964570 0.9977508 0.9839587 0.9811215 0.9867678 0.9305556 0.9722222 0.8888889 0.9857143 1.0000000 0.9714286 1589409197 0.9995422 0.9993638 0.9997205 0.9981866 1.0000000 0.9963912 0.9444444 0.9444444 0.9444444 0.9571429 0.9428571 0.9714286
13 cfsSMOTE_sig Yes Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p 1589408941 0.9971039 0.9964570 0.9977508 0.9839587 0.9811215 0.9867678 0.9305556 0.9722222 0.8888889 0.9857143 1.0000000 0.9714286 1589409218 0.9995422 0.9993638 0.9997205 0.9981866 1.0000000 0.9963912 0.9444444 0.9444444 0.9444444 0.9571429 0.9428571 0.9714286
14 fcfsSMOTE Yes Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.708.3p + hsa.miR.375.3p + hsa.miR.30e.3p 1589408964 0.9971039 0.9964570 0.9977508 0.9839587 0.9811215 0.9867678 0.9305556 0.9722222 0.8888889 0.9857143 1.0000000 0.9714286 1589409238 0.9995422 0.9993638 0.9997205 0.9981866 1.0000000 0.9963912 0.9444444 0.9444444 0.9444444 0.9571429 0.9428571 0.9714286

Description of columns:

By this logic every parameter is also calculated from testing (_test_) and validation (_valid_) set. If the method generated a probability, a default cutoff is used for all of the predictions.

Let’s see the general performance (accuracy) of methods in the benchmark:

metody = OmicSelector_get_benchmark_methods("benchmark.csv")  # gets the methods used in benchmark
par(mfrow = c(2, 2))
for (i in 1:length(metody)) {
    temp = OmicSelector_get_benchmark("benchmark.csv")  # loads benchmark
    temp2 = dplyr::select(temp, starts_with(paste0(metody[i], "_")))
    boxplot(temp[, paste0(metody[i], "_train_Accuracy")], temp[, paste0(metody[i], "_test_Accuracy")], temp[, paste0(metody[i], "_valid_Accuracy")], main = paste0("Method: ", 
        metody[i]), names = c("Training", "Testing", "Validation"), ylab = "Accuracy", ylim = c(0.5, 1))
    tempids = c(match(paste0(metody[i], "_train_Accuracy"), colnames(temp)), match(paste0(metody[i], "_test_Accuracy"), colnames(temp)), match(paste0(metody[i], 
        "_valid_Accuracy"), colnames(temp)))
}
par(mfrow = c(1, 1))

With OmicSelector package, the final optimal feature signature can be selected in 3 ways:

1. Picking the signture which achived the best accuracy in training, testing and validation: (metaindex = mean of all 3 accuracy metrics)

acc1 = OmicSelector_best_signiture_proposals(benchmark_csv = "benchmark.csv", without_train = F)  # generates the benchmark sorted by metaindex
best_signatures = acc1[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])
metaindex method miRy
0.9704465 topFCSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
0.9666671 cfsSMOTE Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p
0.9666671 cfsSMOTE_sig Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p

2. Picking the signture which achived the best accuracy in testing and validation: (metaindex = mean of 2 accuracy metrics)

acc1 = OmicSelector_best_signiture_proposals(benchmark_csv = "benchmark.csv", without_train = T)  # generates the benchmark sorted by metaindex
best_signatures = acc1[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])
metaindex method miRy
0.9580357 topFC Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
0.9579365 topFCSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
0.9544643 cfsSMOTE Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p

3. The signture which achived the best sensitivity and specificity in validation: (metaindex = mean of sensivitiy and specificity in validation dataset)

acc = OmicSelector_best_signiture_proposals_meta11(benchmark_csv = "benchmark.csv")  # generates the benchmark sorted by metaindex
best_signatures = acc[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])
metaindex method miRy
0.9571429 cfs_sig Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p
0.9571429 topFC Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
0.9428571 topFCSMOTE Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p

It is a good practice to assess learning performance for considered signatures across different classification methods. Here, we visualize the over/underfitting of selected methods by comparing accuracy score between testing and validation sets for 5 top scoring signatures across selection of model architectures.

for (i in 1:length(metody)) {
    suppressMessages(library(PairedData))
    suppressMessages(library(profileR))
    pd = paired(as.numeric(acc[1:5, paste0(metody[i], "_train_Accuracy")]), as.numeric(acc[1:5, paste0(metody[i], "_test_Accuracy")]))
    colnames(pd) = c("Train Acc", "Test Acc")
    plot2 = OmicSelector_profileplot(pd, Method.id = acc$method[1:5], standardize = F)
    pd = paired(as.numeric(acc[1:5, paste0(metody[i], "_train_Accuracy")]), as.numeric(acc[1:5, paste0(metody[i], "_valid_Accuracy")]))
    colnames(pd) = c("Train Acc", "Valid Acc")
    plot3 = OmicSelector_profileplot(pd, Method.id = acc$method[1:5], standardize = F)
    pd = paired(as.numeric(acc[1:5, paste0(metody[i], "_test_Accuracy")]), as.numeric(acc[1:5, paste0(metody[i], "_valid_Accuracy")]))
    colnames(pd) = c("Test Acc", "Valid Acc")
    plot4 = OmicSelector_profileplot(pd, Method.id = acc$method[1:5], standardize = F)
    
    
    
    require(gridExtra)
    grid.arrange(arrangeGrob(plot2, plot3, ncol = 2, nrow = 1, top = metody[i]))
    grid.arrange(arrangeGrob(plot4, ncol = 1, nrow = 1, top = metody[i]))
}

The relationship betweend accuracy on testing and validation sets can also be pictured as scatterplot:

acc2 = acc[1:6, ]  # get top 6 methods
accmelt = melt(acc2, id.vars = "method") %>% filter(variable != "metaindex") %>% filter(variable != "miRy")
accmelt = cbind(accmelt, strsplit2(accmelt$variable, "_"))
acctest = accmelt$value[accmelt$`2` == "test"]
accvalid = accmelt$value[accmelt$`2` == "valid"]
accmeth = accmelt$method[accmelt$`2` == "test"]
unique(accmeth)
#> [1] "cfs_sig"      "topFC"        "topFCSMOTE"   "cfsSMOTE"     "cfsSMOTE_sig"
#> [6] "fcfsSMOTE"
plot5 = ggplot(, aes(x = as.numeric(acctest), y = as.numeric(accvalid), shape = accmeth)) + geom_point() + scale_x_continuous(name = "Accuracy on test set", 
    limits = c(0.5, 1)) + scale_y_continuous(name = "Accuracy on validation set", limits = c(0.5, 1)) + theme_bw()
grid.arrange(arrangeGrob(plot5, ncol = 1, nrow = 1))

7 Best signture analysis

Suppose we decide to use sensitivity and specificity in validation set (e.g. in the model architectures we plan to use in our research) as decisive scoring metric for feature signature. The three best signatures may be:

OmicSelector_table(best_signatures[1:3, 2:4])
method SMOTE miRy
cfs_sig No Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p
topFC No Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
topFCSMOTE Yes Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p

To get the miRNAs from formula you can use OmicSelector_get_features_from_benchmark.

selected_miRNAs = OmicSelector_get_features_from_benchmark(benchmark_csv = "benchmark.csv", best_signatures$method[1])  # for the best performing signiture
gsub("\\.", "-", selected_miRNAs)  # R doesn't like hyphens, but we can introduce them easly
#>  [1] "hsa-miR-21-5p"    "hsa-miR-30e-3p"   "hsa-miR-30a-3p"   "hsa-miR-30c-2-3p"
#>  [5] "hsa-miR-132-3p"   "hsa-miR-375-3p"   "hsa-miR-217-5p"   "hsa-miR-338-3p"  
#>  [9] "hsa-miR-199b-5p"  "hsa-miR-381-3p"   "hsa-miR-199a-3p"  "hsa-miR-194-5p"  
#> [13] "hsa-miR-134-5p"   "hsa-miR-192-5p"   "hsa-miR-200a-3p"  "hsa-miR-181c-3p" 
#> [17] "hsa-miR-29a-3p"   "hsa-miR-378a-3p"  "hsa-miR-144-5p"   "hsa-miR-335-3p"  
#> [21] "hsa-miR-126-5p"   "hsa-let-7c-5p"    "hsa-miR-378a-5p"  "hsa-miR-181c-5p" 
#> [25] "hsa-miR-126-3p"   "hsa-miR-185-5p"   "hsa-miR-29c-3p"   "hsa-miR-151a-5p" 
#> [29] "hsa-miR-92b-3p"   "hsa-miR-10b-5p"   "hsa-miR-195-5p"   "hsa-miR-101-3p"  
#> [33] "hsa-miR-484"      "hsa-miR-28-3p"

As a double check, we can inspect the differential expression of miRNAs constituating selected signature:

best_de = OmicSelector_best_signiture_de(selected_miRNAs)
OmicSelector_table(best_de)
miR log2FC p-value BH
1 hsa.miR.21.5p 2.6022157 0.0000000
2 hsa.miR.30e.3p -1.3939819 0.0000000
3 hsa.miR.30a.3p -2.4419651 0.0000000
4 hsa.miR.30c.2.3p -2.0824306 0.0000000
5 hsa.miR.132.3p 1.3642193 0.0000000
6 hsa.miR.375.3p 4.7881053 0.0000000
7 hsa.miR.217.5p 4.9968529 0.0000000
10 hsa.miR.338.3p 1.6447027 0.0000000
11 hsa.miR.199b.5p 2.3814574 0.0000000
13 hsa.miR.381.3p 1.6878957 0.0000000
15 hsa.miR.199a.3p 1.2540293 0.0000000
18 hsa.miR.194.5p 2.9439150 0.0000000
19 hsa.miR.134.5p 1.3684465 0.0000000
23 hsa.miR.192.5p 2.9636965 0.0000000
25 hsa.miR.200a.3p 2.1949415 0.0000000
27 hsa.miR.181c.3p 0.9386203 0.0000000
33 hsa.miR.29a.3p -0.6991346 0.0000000
34 hsa.miR.378a.3p -1.1444252 0.0000000
39 hsa.miR.144.5p -2.1127868 0.0000000
41 hsa.miR.335.3p 1.0571023 0.0000000
42 hsa.miR.126.5p -1.1663511 0.0000000
45 hsa.let.7c.5p -0.8775535 0.0000000
49 hsa.miR.378a.5p -1.0287466 0.0000000
57 hsa.miR.181c.5p 0.8614935 0.0000002
58 hsa.miR.126.3p -0.9851906 0.0000005
61 hsa.miR.185.5p 0.6922687 0.0000020
62 hsa.miR.29c.3p -0.7856959 0.0000026
65 hsa.miR.151a.5p 0.5057800 0.0000040
73 hsa.miR.92b.3p 0.7783325 0.0000088
77 hsa.miR.10b.5p -1.2777969 0.0000396
84 hsa.miR.195.5p -0.7802161 0.0003412
90 hsa.miR.101.3p -0.5956161 0.0015624
106 hsa.miR.484 -0.3113168 0.0182773
113 hsa.miR.28.3p -0.2419443 0.0355939

Let’s visualize the performance of those methods using barplots:

for (i in 1:3) {
    cat(paste0("\n\n## ", acc$method[i], "\n\n"))
    par(mfrow = c(1, 2))
    acc = OmicSelector_best_signiture_proposals_meta11("benchmark.csv")
    metody = OmicSelector_get_benchmark_methods("benchmark.csv")
    ktory_set = match(acc$method[i], OmicSelector_get_benchmark("benchmark.csv")$method)
    # do_ktorej_kolumny = which(colnames(acc) == 'metaindex') barplot(as.numeric(acc[i,1:do_ktorej_kolumny]))
    for (ii in 1:length(metody)) {
        
        temp = OmicSelector_get_benchmark("benchmark.csv") %>% dplyr::select(starts_with(paste0(metody[ii], "_t")), starts_with(paste0(metody[ii], "_v")))
        
        ROCtext = paste0("Training AUC ROC: ", round(temp[ktory_set, 1], 2), " (95%CI: ", round(temp[ktory_set, 2], 2), "-", round(temp[ktory_set, 3], 
            2), ")")
        
        temp = temp[, -c(1:3)]
        temp2 = as.numeric(temp[ktory_set, ])
        temp3 = matrix(temp2, nrow = 3, byrow = T)
        colnames(temp3) = c("Accuracy", "Sensitivity", "Specificity")
        rownames(temp3) = c("Training", "Testing", "Validation")
        temp3 = t(temp3)
        
        plot1 = barplot(temp3, beside = T, ylim = c(0, 1), xlab = paste0(ROCtext, "\nBlack - accuracy, blue - sensitivity, green - specificity"), width = 0.85, 
            col = c("black", "blue", "green"), legend = F, args.legend = list(x = "topright", bty = "n", inset = c(0, -0.25)), cex.lab = 0.7, main = paste0(acc$method[i], 
                " - ", metody[ii]), font.lab = 2)
        ## Add text at top of bars
        text(x = plot1, y = as.numeric(temp3), label = paste0(round(as.numeric(temp[ktory_set, ]) * 100, 1), "%"), pos = 3, cex = 0.6, col = "red")
    }
    par(mfrow = c(1, 1))
    
}
#> 
#> 
#> ## cfs_sig

#> 
#> 
#> ## topFC

#> 
#> 
#> ## topFCSMOTE

Finally, we can assess the overlap of top 3 feature selection methods:

overlap = OmicSelector_signiture_overlap(acc$method[1:3], "benchmark.csv")

Which 3 miRNAs are common for all 3 signatures?

attr(overlap, "intersections")[4]
#> $topFC
#> [1] "hsa.miR.708.3p" "hsa.miR.141.3p"

Let’s draw vulcano plot and mark the miRNAs selected in best signature:

OmicSelector_vulcano_plot(selected_miRNAs = de$miR, DE = de, only_label = selected_miRNAs)

Let’s draw heatmap for selected miRNAs in whole dataset (training, testing and validation set).

OmicSelector_heatmap(x = dplyr::select(mixed, gsub("\\.", "-", selected_miRNAs)), rlab = data.frame(Class = mixed$Class, Mix = mixed$mix), zscore = F, margins = c(10, 
    10))

OmicSelector_heatmap(x = dplyr::select(mixed, gsub("\\.", "-", selected_miRNAs)), rlab = data.frame(Class = mixed$Class, Mix = mixed$mix), zscore = T, margins = c(10, 
    10))

Based on everything we have done so far, we suggest using the following signiture in further validation of biomarker study.

cat(paste0(gsub("\\.", "-", selected_miRNAs), collapse = ", "))
#> hsa-miR-21-5p, hsa-miR-30e-3p, hsa-miR-30a-3p, hsa-miR-30c-2-3p, hsa-miR-132-3p, hsa-miR-375-3p, hsa-miR-217-5p, hsa-miR-338-3p, hsa-miR-199b-5p, hsa-miR-381-3p, hsa-miR-199a-3p, hsa-miR-194-5p, hsa-miR-134-5p, hsa-miR-192-5p, hsa-miR-200a-3p, hsa-miR-181c-3p, hsa-miR-29a-3p, hsa-miR-378a-3p, hsa-miR-144-5p, hsa-miR-335-3p, hsa-miR-126-5p, hsa-let-7c-5p, hsa-miR-378a-5p, hsa-miR-181c-5p, hsa-miR-126-3p, hsa-miR-185-5p, hsa-miR-29c-3p, hsa-miR-151a-5p, hsa-miR-92b-3p, hsa-miR-10b-5p, hsa-miR-195-5p, hsa-miR-101-3p, hsa-miR-484, hsa-miR-28-3p

8 Sesssion

session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.2 (2019-12-12)
#>  os       Ubuntu 18.04.4 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       Europe/Warsaw               
#>  date     2020-05-14                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package          * version    date       lib source                       
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#>  manipulateWidget   0.10.1     2020-02-24 [1] CRAN (R 3.6.2)               
#>  MASS             * 7.3-51.6   2020-04-26 [1] CRAN (R 3.6.2)               
#>  MatchIt          * 3.0.2      2018-01-09 [1] CRAN (R 3.6.2)               
#>  Matrix             1.2-18     2019-11-27 [4] CRAN (R 3.6.1)               
#>  matrixStats        0.56.0     2020-03-13 [1] CRAN (R 3.6.2)               
#>  memoise            1.1.0      2017-04-21 [1] CRAN (R 3.6.0)               
#>  mice             * 3.8.0      2020-02-21 [1] CRAN (R 3.6.2)               
#>  mime               0.9        2020-02-04 [1] CRAN (R 3.6.2)               
#>  miniUI             0.1.1.1    2018-05-18 [1] CRAN (R 3.6.0)               
#>  minqa              1.2.4      2014-10-09 [1] CRAN (R 3.6.0)               
#>  OmicSelector    * 0.1.0      2020-05-13 [1] local                        
#>  mnormt             1.5-7      2020-04-30 [1] CRAN (R 3.6.2)               
#>  ModelMetrics       1.2.2.2    2020-03-17 [1] CRAN (R 3.6.2)               
#>  modelr             0.1.7      2020-04-30 [1] CRAN (R 3.6.2)               
#>  modeltools         0.2-23     2020-03-05 [1] CRAN (R 3.6.2)               
#>  multcomp           1.4-13     2020-04-08 [1] CRAN (R 3.6.2)               
#>  munsell            0.5.0      2018-06-12 [1] CRAN (R 3.6.0)               
#>  mvtnorm          * 1.1-0      2020-02-24 [1] CRAN (R 3.6.2)               
#>  nlme               3.1-147    2020-04-13 [4] CRAN (R 3.6.2)               
#>  nloptr             1.2.2.1    2020-03-11 [1] CRAN (R 3.6.2)               
#>  nnet             * 7.3-14     2020-04-26 [4] CRAN (R 3.6.2)               
#>  numDeriv           2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0)               
#>  PairedData       * 1.1.1      2018-06-02 [1] CRAN (R 3.6.2)               
#>  pamr               1.56.1     2019-04-22 [1] CRAN (R 3.6.1)               
#>  party              1.3-4      2020-03-05 [1] CRAN (R 3.6.2)               
#>  partykit           1.2-7      2020-03-06 [1] CRAN (R 3.6.2)               
#>  pbivnorm           0.6.0      2015-01-23 [1] CRAN (R 3.6.1)               
#>  pillar             1.4.4      2020-05-05 [1] CRAN (R 3.6.2)               
#>  pkgbuild           1.0.8      2020-05-07 [1] CRAN (R 3.6.2)               
#>  pkgconfig          2.0.3      2019-09-22 [1] CRAN (R 3.6.1)               
#>  pkgload            1.0.2      2018-10-29 [1] CRAN (R 3.6.0)               
#>  plotly           * 4.9.2.1    2020-04-04 [1] CRAN (R 3.6.2)               
#>  plyr             * 1.8.6      2020-03-03 [1] CRAN (R 3.6.2)               
#>  prettyunits        1.1.1      2020-01-24 [1] CRAN (R 3.6.2)               
#>  pROC             * 1.16.2     2020-03-19 [1] CRAN (R 3.6.2)               
#>  processx           3.4.2      2020-02-09 [1] CRAN (R 3.6.2)               
#>  prodlim            2019.11.13 2019-11-17 [1] CRAN (R 3.6.1)               
#>  profileR         * 0.3-5      2018-04-19 [1] CRAN (R 3.6.2)               
#>  promises           1.1.0      2019-10-04 [1] CRAN (R 3.6.1)               
#>  ps                 1.3.3      2020-05-08 [1] CRAN (R 3.6.2)               
#>  psych            * 1.9.12.31  2020-01-08 [1] CRAN (R 3.6.2)               
#>  purrr            * 0.3.4      2020-04-17 [1] CRAN (R 3.6.2)               
#>  quantmod           0.4.17     2020-03-31 [1] CRAN (R 3.6.2)               
#>  R.methodsS3      * 1.8.0      2020-02-14 [1] CRAN (R 3.6.2)               
#>  R.oo             * 1.23.0     2019-11-03 [1] CRAN (R 3.6.1)               
#>  R.utils          * 2.9.2      2019-12-08 [1] CRAN (R 3.6.2)               
#>  R6                 2.4.1      2019-11-12 [1] CRAN (R 3.6.1)               
#>  randomForest     * 4.6-14     2018-03-25 [1] CRAN (R 3.6.2)               
#>  rappdirs           0.3.1      2016-03-28 [1] CRAN (R 3.6.1)               
#>  RColorBrewer     * 1.1-2      2014-12-07 [1] CRAN (R 3.6.0)               
#>  Rcpp             * 1.0.4.6    2020-04-09 [1] CRAN (R 3.6.2)               
#>  readr            * 1.3.1      2018-12-21 [1] CRAN (R 3.6.1)               
#>  readxl             1.3.1      2019-03-13 [1] CRAN (R 3.6.0)               
#>  recipes            0.1.12     2020-05-01 [1] CRAN (R 3.6.2)               
#>  remotes          * 2.1.1      2020-02-15 [1] CRAN (R 3.6.2)               
#>  reprex             0.3.0      2019-05-16 [1] CRAN (R 3.6.1)               
#>  reshape          * 0.8.8      2018-10-23 [1] CRAN (R 3.6.0)               
#>  reshape2           1.4.4      2020-04-09 [1] CRAN (R 3.6.2)               
#>  reticulate       * 1.15       2020-04-02 [1] CRAN (R 3.6.2)               
#>  rgl                0.100.54   2020-04-14 [1] CRAN (R 3.6.2)               
#>  rJava              0.9-12     2020-03-24 [1] CRAN (R 3.6.2)               
#>  rlang              0.4.6      2020-05-02 [1] CRAN (R 3.6.2)               
#>  rmarkdown        * 2.1        2020-01-20 [1] CRAN (R 3.6.2)               
#>  ROCR               1.0-11     2020-05-02 [1] CRAN (R 3.6.2)               
#>  ROSE             * 0.0-3      2014-07-15 [1] CRAN (R 3.6.2)               
#>  rpart              4.1-15     2019-04-12 [1] CRAN (R 3.6.2)               
#>  rprojroot          1.3-2      2018-01-03 [1] CRAN (R 3.6.0)               
#>  rsq              * 2.0        2020-05-09 [1] CRAN (R 3.6.2)               
#>  rstudioapi         0.11       2020-02-07 [1] CRAN (R 3.6.2)               
#>  rvest              0.3.5      2019-11-08 [1] CRAN (R 3.6.1)               
#>  RWeka              0.4-42     2020-02-02 [1] CRAN (R 3.6.2)               
#>  RWekajars          3.9.3-2    2019-10-19 [1] CRAN (R 3.6.1)               
#>  sandwich           2.5-1      2019-04-06 [1] CRAN (R 3.6.0)               
#>  scales           * 1.1.1      2020-05-11 [1] CRAN (R 3.6.2)               
#>  sessioninfo        1.1.1      2018-11-05 [1] CRAN (R 3.6.0)               
#>  shiny              1.4.0.2    2020-03-13 [1] CRAN (R 3.6.2)               
#>  stargazer        * 5.2.2      2018-05-30 [1] CRAN (R 3.6.2)               
#>  statmod            1.4.34     2020-02-17 [1] CRAN (R 3.6.2)               
#>  stringi            1.4.6      2020-02-17 [1] CRAN (R 3.6.2)               
#>  stringr          * 1.4.0      2019-02-10 [1] CRAN (R 3.6.2)               
#>  strucchange        1.5-2      2019-10-12 [1] CRAN (R 3.6.1)               
#>  survival         * 3.1-12     2020-04-10 [1] CRAN (R 3.6.2)               
#>  testthat           2.3.2      2020-03-02 [1] CRAN (R 3.6.2)               
#>  TH.data            1.0-10     2019-01-21 [1] CRAN (R 3.6.0)               
#>  tibble           * 3.0.1      2020-04-20 [1] CRAN (R 3.6.2)               
#>  tidyr            * 1.0.3      2020-05-07 [1] CRAN (R 3.6.2)               
#>  tidyselect         1.1.0      2020-05-11 [1] CRAN (R 3.6.2)               
#>  tidyverse        * 1.3.0      2019-11-21 [1] CRAN (R 3.6.2)               
#>  timeDate           3043.102   2018-02-21 [1] CRAN (R 3.6.0)               
#>  TTR                0.23-6     2019-12-15 [1] CRAN (R 3.6.1)               
#>  usethis          * 1.6.1      2020-04-29 [1] CRAN (R 3.6.2)               
#>  vctrs              0.3.0      2020-05-11 [1] CRAN (R 3.6.2)               
#>  viridisLite        0.3.0      2018-02-01 [1] CRAN (R 3.6.0)               
#>  webshot            0.5.2      2019-11-22 [1] CRAN (R 3.6.1)               
#>  withr              2.2.0      2020-04-20 [1] CRAN (R 3.6.2)               
#>  xfun               0.13       2020-04-13 [1] CRAN (R 3.6.2)               
#>  xml2               1.3.2      2020-04-23 [1] CRAN (R 3.6.2)               
#>  xtable             1.8-4      2019-04-21 [1] CRAN (R 3.6.0)               
#>  xts                0.12-0     2020-01-19 [1] CRAN (R 3.6.2)               
#>  yaml               2.2.1      2020-02-01 [1] CRAN (R 3.6.2)               
#>  zoo                1.8-8      2020-05-02 [1] CRAN (R 3.6.2)               
#> 
#> [1] /home/konrad/R/x86_64-pc-linux-gnu-library/3.6
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library

To render this tutorial we used:

render("Tutorial.Rmd", output_file = "Tutorial.html", output_dir = "../static/")

Packages installed in our docker enviorment:

OmicSelector_table(as.data.frame(installed.packages()))
Package LibPath Version Priority Depends Imports LinkingTo Suggests Enhances License License_is_FOSS License_restricts_use OS_type MD5sum NeedsCompilation Built
abind abind /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-5 NA R (>= 1.5.0) methods, utils NA NA NA LGPL (>= 2) NA NA NA NA no 3.6.0
acepack acepack /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.1 NA NA NA NA testthat NA MIT + file LICENSE NA NA NA NA yes 3.6.0
ada ada /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0-5 NA R(>= 2.10),rpart NA NA NA NA GPL NA NA NA NA no 3.6.1
additivityTests additivityTests /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-4 NA NA NA NA knitr NA GPL-3 NA NA NA NA no 3.6.1
ade4 ade4 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7-15 NA R (>= 2.10) graphics, grDevices, methods, stats, utils, MASS, pixmap, sp NA ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir, lattice, spdep, splancs, waveslim NA GPL (>= 2) NA NA NA NA yes 3.6.2
affy affy /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.62.0 NA R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc preprocessCore tkWidgets (>= 1.19.0), affydata, widgetTools NA LGPL (>= 2.0) NA NA NA NA yes 3.6.1
affyio affyio /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.54.0 NA R (>= 2.6.0) zlibbioc, methods NA NA NA LGPL (>= 2) NA NA NA NA yes 3.6.1
ALL ALL /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.26.0 NA R (>= 2.10), Biobase (>= 2.5.5) NA NA rpart NA Artistic-2.0 NA NA NA NA no 3.6.1
amap amap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.8-18 NA R (>= 3.6.0) NA NA Biobase NA GPL NA NA NA NA yes 3.6.1
annotate annotate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.62.0 NA R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), RCurl NA hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, NA Artistic-2.0 NA NA NA NA no 3.6.0
AnnotationDbi AnnotationDbi /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.46.1 NA R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges DBI, RSQLite, S4Vectors (>= 0.9.25) NA hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr NA Artistic-2.0 NA NA NA NA no 3.6.1
ape ape /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.3 NA R (>= 3.2.0) nlme, lattice, graphics, methods, stats, tools, utils, parallel, Rcpp (>= 0.12.0) Rcpp gee, expm, igraph NA GPL (>= 2) NA NA NA NA yes 3.6.1
apeglm apeglm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.0 NA NA emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp Rcpp, RcppEigen, RcppNumerical DESeq2, airway, knitr, rmarkdown, testthat NA GPL-2 NA NA NA NA yes 3.6.1
aroma.light aroma.light /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.14.0 NA R (>= 2.15.2) stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.22.0), R.utils (>= 2.7.0), matrixStats (>= 0.54.0) NA princurve (>= 2.1.2) NA GPL (>= 2) NA NA NA NA no 3.6.1
arules arules /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6-5 NA R (>= 3.4.0), Matrix (>= 1.2-0) stats, methods, graphics, utils NA pmml, XML, arulesViz, testthat NA GPL-3 NA NA NA NA yes 3.6.2
arulesViz arulesViz /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-3 NA arules (>= 1.4.1), grid scatterplot3d, vcd, seriation, igraph (>= 1.0.0), graphics, methods, utils, grDevices, stats, colorspace, DT, plotly, visNetwork NA graph, Rgraphviz, iplots, shiny, shinythemes, htmlwidgets NA GPL-3 NA NA NA NA no 3.6.1
askpass askpass /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1 NA NA sys (>= 2.1) NA testthat NA MIT + file LICENSE NA NA NA NA yes 3.6.0
assertive assertive /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3-5 NA R (>= 3.0.0) assertive.base (>= 0.0-4), assertive.properties (>= 0.0-2), assertive.types (>= 0.0-2), assertive.numbers, assertive.strings, assertive.datetimes, assertive.files, assertive.sets (>= 0.0-2), assertive.matrices, assertive.models, assertive.data, assertive.data.uk, assertive.data.us, assertive.reflection (>= 0.0-2), assertive.code, knitr NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.base assertive.base /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-7 NA R (>= 3.0.0) methods, utils NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.code assertive.code /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.properties, assertive.types, methods NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.data assertive.data /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.strings NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.data.uk assertive.data.uk /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.strings NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.data.us assertive.data.us /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.strings NA testthat, devtools NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.datetimes assertive.datetimes /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.types NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.files assertive.files /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.numbers NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.matrices assertive.matrices /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2) NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.models assertive.models /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2), stats NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.numbers assertive.numbers /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-2 NA R (>= 3.0.0) assertive.base (>= 0.0-2) NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.properties assertive.properties /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-4 NA R (>= 3.0.0) assertive.base (>= 0.0-7), methods NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.reflection assertive.reflection /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-4 NA R (>= 3.0.0) assertive.base (>= 0.0-7), utils NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.sets assertive.sets /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-7) NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.strings assertive.strings /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-2), assertive.types, stringi NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
assertive.types assertive.types /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-3 NA R (>= 3.0.0) assertive.base (>= 0.0-7), assertive.properties, codetools, methods, stats NA testthat, data.table, dplyr, xml2 NA GPL (>= 3) NA NA NA NA no 3.6.1
assertthat assertthat /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.1 NA NA tools NA testthat, covr NA GPL-3 NA NA NA NA no 3.6.0
backports backports /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.6 NA R (>= 3.0.0) utils NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
bartMachine bartMachine /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.4.2 NA R (>= 2.14.0), rJava (>= 0.9-8), bartMachineJARs (>= 1.0), car, randomForest, missForest graphics, grDevices, stats NA NA NA GPL-3 NA NA NA NA no 3.6.0
bartMachineJARs bartMachineJARs /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1 NA R (>= 2.14.0), rJava (>= 0.9-8) NA NA NA NA GPL-3 NA NA NA NA no 3.6.0
base64enc base64enc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-3 NA R (>= 2.9.0) NA NA NA png GPL-2 | GPL-3 NA NA NA NA yes 3.6.0
BBmisc BBmisc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.11 NA NA utils, methods, stats, checkmate (>= 1.8.0) NA testthat, microbenchmark, codetools NA BSD_2_clause + file LICENSE NA NA NA NA yes 3.6.1
bbmle bbmle /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.23.1 NA R (>= 3.0.0), stats4 stats, numDeriv, lattice, MASS, methods, bdsmatrix, Matrix, mvtnorm NA emdbook, rms, ggplot2, RUnit, MuMIn, AICcmodavg, Hmisc, optimx (>= 2013.8.6), knitr, testthat NA GPL NA NA NA NA no 3.6.2
bdsmatrix bdsmatrix /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-4 NA methods, R (>= 2.0.0) NA NA NA NA LGPL-2 NA NA NA NA yes 3.6.1
beachmat beachmat /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.0 NA NA methods, DelayedArray, BiocGenerics NA testthat, BiocStyle, knitr, rmarkdown, Matrix, devtools NA GPL-3 NA NA NA NA yes 3.6.0
beeswarm beeswarm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.3 NA NA stats, graphics, grDevices, utils NA NA NA Artistic-2.0 NA NA NA NA no 3.6.0
bench bench /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.1 NA R (>= 3.1) glue, methods, pillar, profmem, rlang (>= 0.2.0), stats, tibble, utils NA covr, dplyr, forcats, ggbeeswarm, ggplot2, ggridges, mockery, parallel, scales, testthat, tidyr (>= 0.8.1), vctrs, withr NA GPL-3 NA NA NA NA yes 3.6.1
bestNormalize bestNormalize /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5.0 NA R (>= 3.1.0) LambertW, nortest, dplyr, doParallel, foreach, doRNG, recipes, tibble NA knitr, rmarkdown, MASS, testthat, mgcv, parallel NA GPL-3 NA NA NA NA no 3.6.2
BGLR BGLR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.8 NA R (>= 3.5.0) truncnorm NA NA NA GPL-3 NA NA NA NA yes 3.6.1
BH BH /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.72.0-3 NA NA NA NA NA NA BSL-1.0 NA NA NA NA no 3.6.1
bibtex bibtex /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.2.2 NA R (>= 3.0.2) stringr, utils NA testthat NA GPL (>= 2) NA NA NA NA yes 3.6.1
biclust biclust /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.2 NA R (>= 2.10), MASS, grid, colorspace, lattice methods, flexclust, additivityTests, tidyr, ggplot2 NA isa2 NA GPL-3 NA NA NA NA yes 3.6.2
Biobase Biobase /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.44.0 NA R (>= 2.10), BiocGenerics (>= 0.27.1), utils methods NA tools, tkWidgets, ALL, RUnit, golubEsets NA Artistic-2.0 NA NA NA NA yes 3.6.0
BiocGenerics BiocGenerics /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.30.0 NA R (>= 3.6.0), methods, utils, graphics, stats, parallel methods, utils, graphics, stats, parallel NA Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit NA Artistic-2.0 NA NA NA NA no 3.6.0
BiocManager BiocManager /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.30.10 NA NA utils NA BiocStyle, BiocVersion, remotes, testthat, withr, curl, knitr NA Artistic-2.0 NA NA NA NA no 3.6.1
BiocNeighbors BiocNeighbors /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.0 NA NA Rcpp, BiocGenerics, S4Vectors, BiocParallel, stats, methods Rcpp, RcppAnnoy, RcppHNSW testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW NA GPL-3 NA NA NA NA yes 3.6.0
Biocomb Biocomb /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4 NA R (>= 2.13.0),gtools,Rcpp (>= 0.12.1) rgl, MASS, e1071, randomForest, pROC, ROCR, arules, pamr, class, nnet, rpart, FSelector, RWeka, grDevices, graphics, stats, utils Rcpp NA NA GPL (>= 3) NA NA NA NA yes 3.6.2
BiocParallel BiocParallel /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.18.1 NA methods stats, utils, futile.logger, parallel, snow BH BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
BiocSingular BiocSingular /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA NA BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, irlba, rsvd, Rcpp Rcpp, beachmat testthat, BiocStyle, knitr, rmarkdown, beachmat NA GPL-3 NA NA NA NA yes 3.6.0
BiocStyle BiocStyle /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.12.0 NA NA bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager NA BiocGenerics, RUnit, htmltools NA Artistic-2.0 NA NA NA NA no 3.6.2
BiocVersion BiocVersion /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.9.0 NA R (>= 3.6.0), R (< 3.7.0) NA NA NA NA Artistic-2.0 NA NA NA NA no 3.6.0
biomaRt biomaRt /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.40.5 NA methods utils, XML, RCurl, AnnotationDbi, progress, stringr, httr NA annotate, BiocStyle, knitr, rmarkdown, testthat NA Artistic-2.0 NA NA NA NA no 3.6.1
biostatUZH biostatUZH /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.8.0 NA R (>= 2.15.0), grDevices, graphics, stats, survival (>= 2.35) boot NA cmprsk, lme4, prodlim, psy, xtable, reporttools, Hmisc, surveillance, carData MASS, ellipse GPL (>=2) NA NA NA NA no 3.6.2
Biostrings Biostrings /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.52.0 NA R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13), IRanges, XVector (>= 0.23.2) graphics, methods, stats, utils S4Vectors, IRanges, XVector BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit Rmpi Artistic-2.0 NA NA NA NA yes 3.6.1
bit bit /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-15.2 NA R (>= 2.9.2) NA NA NA NA GPL-2 NA NA NA NA yes 3.6.2
bit64 bit64 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-7 NA R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats NA NA NA NA GPL-2 NA NA NA NA yes 3.6.0
bitops bitops /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-6 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.0
blob blob /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.1 NA NA methods, rlang, vctrs (>= 0.2.1) NA covr, crayon, pillar (>= 1.2.1), testthat NA GPL-3 NA NA NA NA no 3.6.2
bmp bmp /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3 NA NA NA NA pixmap, testthat NA GPL (>= 2) NA NA NA NA no 3.6.1
bookdown bookdown /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.18 NA NA htmltools (>= 0.3.6), knitr (>= 1.22), rmarkdown (>= 2.0), xfun (>= 0.6), tinytex (>= 0.12) NA htmlwidgets, rstudioapi, miniUI, rsconnect (>= 0.4.3), servr (>= 0.13), shiny, testit (>= 0.9), tufte, webshot NA GPL-3 NA NA NA NA no 3.6.2
bootstrap bootstrap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2019.6 NA stats, R (>= 2.10.0) NA NA NA NA BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.0
Boruta Boruta /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 6.0.0 NA ranger NA NA mlbench, rFerns, randomForest, testthat, xgboost NA GPL (>= 2) NA NA NA NA no 3.6.2
bounceR bounceR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1 NA R (>= 3.4.3) purrr, furrr, parallel, mboost, strucchange, np, reshape2, ggplot2, mRMRe, dplyr, future NA NA NA MIT + file LICENSE NA NA NA NA no 3.6.1
BradleyTerry2 BradleyTerry2 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-2 NA R (>= 2.10) brglm, gtools, lme4 (>= 1.0), qvcalc, stats NA prefmod, testthat gnm GPL (>= 2) NA NA NA NA no 3.6.2
brew brew /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-6 NA NA NA NA NA NA GPL-2 NA NA NA NA NA 3.6.1
brglm brglm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.2 NA R (>= 2.6.0), profileModel NA NA MASS NA GPL (>= 2) NA NA NA NA yes 3.6.1
broom broom /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.6 NA R (>= 3.1) backports, dplyr, generics (>= 0.0.2), methods, nlme, purrr, reshape2, stringr, tibble (>= 3.0.0), tidyr NA AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot, brms, btergm, car, caret, coda, covr, e1071, emmeans, ergm, gam (>= 1.15), gamlss, gamlss.data, gamlss.dist, geepack, ggplot2, glmnet, gmm, Hmisc, irlba, Kendall, knitr, ks, Lahman, lavaan, lfe, lme4, lmodel2, lmtest, lsmeans, maps, maptools, MASS, Matrix, mclust, mgcv, muhaz, multcomp, network, nnet, orcutt (>= 2.2), ordinal, plm, plyr, poLCA, psych, quantreg, rgeos, rmarkdown, rsample, rstan, rstanarm, sp, speedglm, statnet.common, survey, survival, testthat, tseries, zoo NA MIT + file LICENSE NA NA NA NA no 3.6.2
C50 C50 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.3 NA R (>= 2.10.0) partykit, Cubist (>= 0.2.3) NA knitr, modeldata NA GPL-3 NA NA NA NA yes 3.6.2
ca ca /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.71.1 NA R (>= 3.0.0) NA NA rgl (>= 0.64-10), vcd NA GPL NA NA NA NA no 3.6.2
Cairo Cairo /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5-12 NA R (>= 2.4.0) grDevices, graphics NA png FastRWeb GPL-2 NA NA NA NA yes 3.6.2
calibrate calibrate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7.5 NA R (>= 3.5.0), MASS NA NA NA NA GPL-2 NA NA NA NA no 3.6.2
callr callr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.4.3 NA NA processx (>= 3.4.0), R6, utils NA cliapp, covr, crayon, fansi, pingr, ps, rprojroot, spelling, testthat, tibble, withr NA MIT + file LICENSE NA NA NA NA no 3.6.2
car car /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0-7 NA R (>= 3.5.0), carData (>= 3.0-0) abind, MASS, mgcv, nnet, pbkrtest (>= 0.4-4), quantreg, grDevices, utils, stats, graphics, maptools, rio, lme4, nlme NA alr4, boot, coxme, knitr, leaps, lmtest, Matrix, MatrixModels, rgl (>= 0.93.960), sandwich, SparseM, survival, survey NA GPL (>= 2) NA NA NA NA no 3.6.2
carData carData /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0-3 NA R (>= 3.0) NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
caret caret /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 6.0-86 NA R (>= 3.2.0), lattice (>= 0.20), ggplot2 foreach, methods, plyr, ModelMetrics (>= 1.2.2.2), nlme, reshape2, stats, stats4, utils, grDevices, recipes (>= 0.1.10), withr (>= 2.0.0), pROC, NA BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam (>= 1.15), ipred, kernlab, knitr, klaR, MASS, ellipse, mda, mgcv, mlbench, MLmetrics, nnet, party (>= 0.9-99992), pls, proxy, randomForest, RANN, spls, subselect, pamr, superpc, Cubist, testthat (>= 0.9.1), rpart, dplyr, covr NA GPL (>= 2) NA NA NA NA yes 3.6.2
caretEnsemble caretEnsemble /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.1 NA R (>= 3.2.0) methods, pbapply, ggplot2, digest, plyr, lattice, gridExtra, data.table, caret NA caTools, testthat, lintr, randomForest, glmnet, rpart, kernlab, nnet, e1071, ipred, pROC, knitr, mlbench, MASS, gbm, klaR, rmarkdown NA MIT + file LICENSE NA NA NA NA no 3.6.1
caTools caTools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.18.0 NA R (>= 3.6.0) bitops NA MASS, rpart NA GPL-3 NA NA NA NA yes 3.6.1
cba cba /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2-21 NA R (>= 2.10), grid, proxy stats, graphics, grDevices, methods NA gclus, colorspace NA GPL-2 NA NA NA NA yes 3.6.1
cellranger cellranger /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA R (>= 3.0.0) rematch, tibble NA covr, testthat (>= 1.0.0), knitr, rmarkdown NA MIT + file LICENSE NA NA NA NA no 3.6.0
CGEN CGEN /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.20.0 NA R (>= 2.10.1), survival, mvtnorm NA NA cluster NA GPL-2 + file LICENSE NA NA NA NA yes 3.6.0
checkmate checkmate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.0 NA R (>= 3.0.0) backports (>= 1.1.0), utils NA R6, fastmatch, data.table (>= 1.9.8), devtools, ggplot2, knitr, magrittr, microbenchmark, rmarkdown, testthat (>= 0.11.0), tinytest (>= 1.1.0), tibble NA BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.2
chron chron /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3-55 NA R (>= 2.12.0) graphics, stats NA scales, ggplot2 zoo GPL-2 NA NA NA NA yes 3.6.2
circlize circlize /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.9 NA R (>= 3.0.0), graphics GlobalOptions (>= 0.1.0), shape, grDevices, utils, stats, colorspace, methods, grid NA knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 2.0.0), gridBase, png NA MIT + file LICENSE NA NA NA NA no 3.6.2
CircStats CircStats /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2-6 NA MASS, boot NA NA NA NA GPL-2 NA NA NA NA no 3.6.1
classInt classInt /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-3 NA R (>= 2.2) grDevices, stats, graphics, e1071, class, KernSmooth NA spData (>= 0.2.6.2), units, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 3.6.2
cli cli /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.2 NA R (>= 2.10) assertthat, crayon (>= 1.3.4), glue, methods, utils, fansi NA callr, covr, htmlwidgets, knitr, mockery, rmarkdown, rstudioapi, prettycode (>= 1.1.0), testthat, withr NA MIT + file LICENSE NA NA NA NA no 3.6.2
clipr clipr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7.0 NA NA utils NA covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>= 2.0.0) NA GPL-3 NA NA NA NA no 3.6.1
clisymbols clisymbols /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.0 NA NA NA NA testthat NA MIT + file LICENSE NA NA NA NA no 3.6.0
clue clue /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3-57 NA R (>= 3.2.0) stats, cluster, graphics, methods NA e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations RWeka, ape, cba, cclust, flexclust, flexmix, kernlab, mclust, movMF, modeltools GPL-2 NA NA NA NA yes 3.6.1
cluster cluster /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1.0 recommended R (>= 3.3.0) graphics, grDevices, stats, utils NA MASS, Matrix NA GPL (>= 2) NA NA NA NA yes 3.6.1
clusterProfiler clusterProfiler /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.12.0 NA R (>= 3.4.0) AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7), ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rvcheck, stats, tidyr, utils NA AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat NA Artistic-2.0 NA NA NA NA no 3.6.1
clv clv /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3-2.2 NA cluster, class NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.2
cmprsk cmprsk /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2-9 NA R (>= 3.0.0), survival NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
coda coda /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.19-3 NA R (>= 2.14.0) lattice NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
coin coin /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-1 NA R (>= 3.4.0), survival methods, parallel, stats, stats4, utils, libcoin (>= 1.0-0), matrixStats (>= 0.54.0), modeltools (>= 0.2-9), mvtnorm (>= 1.0-5), multcomp libcoin (>= 1.0-0) xtable, e1071, vcd, TH.data (>= 1.0-7) NA GPL-2 NA NA NA NA yes 3.6.1
colorspace colorspace /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-1 NA R (>= 3.0.0), methods graphics, grDevices, stats NA datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd, tcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg, knitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis, wesanderson NA BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.0
combinat combinat /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-8 NA NA NA NA NA NA GPL-2 NA NA NA NA NA 3.6.0
commonmark commonmark /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7 NA NA NA NA curl, testthat, xml2 NA BSD_2_clause + file LICENSE NA NA NA NA yes 3.6.1
compare compare /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2-6 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
ComplexHeatmap ComplexHeatmap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.0 NA R (>= 3.1.2), methods, grid, graphics, stats, grDevices circlize (>= 0.4.5), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png NA testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges NA MIT + file LICENSE NA NA NA NA no 3.6.1
config config /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3 NA NA yaml (>= 2.1.13) NA testthat, knitr NA GPL-3 NA NA NA NA no 3.6.1
ConsensusClusterPlus ConsensusClusterPlus /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.48.0 NA NA Biobase, ALL, graphics, stats, utils, cluster NA NA NA GPL version 2 NA NA NA NA no 3.6.1
corpcor corpcor /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.9 NA R (>= 3.0.2) stats NA NA GPL (>= 3) NA NA NA NA no 3.6.1
corrplot corrplot /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.84 NA NA NA NA knitr, RColorBrewer, testthat NA GPL NA NA NA NA no 3.6.1
covr covr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.5.0 NA R (>= 3.1.0), methods digest, stats, utils, jsonlite, rex, httr, crayon, withr (>= 1.0.2), yaml NA R6, knitr, rmarkdown, htmltools, DT (>= 0.2), testthat, rlang, rstudioapi (>= 0.2), xml2 (>= 1.0.0), parallel, memoise, mockery NA GPL-3 NA NA NA NA yes 3.6.2
cowplot cowplot /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA R (>= 3.5.0) ggplot2 (> 2.2.1), grid, gtable, grDevices, methods, rlang, scales, utils NA Cairo, covr, dplyr, forcats, gridGraphics (>= 0.4-0), knitr, lattice, magick, maps, PASWR, rmarkdown, testthat (>= 1.0.0), tidyr, vdiffr (>= 0.3.0), VennDiagram NA GPL-2 NA NA NA NA no 3.6.1
cqn cqn /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.30.0 NA R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg splines NA scales, edgeR NA Artistic-2.0 NA NA NA NA no 3.6.1
cr17 cr17 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.0 NA ggplot2 (>= 2.2.1), survival (>= 2.41-3), cmprsk (>= 2.2-7), gridExtra (>= 2.2.1), R (>= 3.3.2) dplyr (>= 0.5.0), scales (>= 0.4.1), grid (>= 3.3.0), gtable (>= 0.2.0) NA knitr, rmarkdown NA GPL NA NA NA NA no 3.6.2
crayon crayon /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.4 NA NA grDevices, methods, utils NA mockery, rstudioapi, testthat, withr NA MIT + file LICENSE NA NA NA NA no 3.6.0
crosstalk crosstalk /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0.1 NA NA htmltools (>= 0.3.6), jsonlite, lazyeval, R6 NA shiny, ggplot2, testthat (>= 2.1.0) NA MIT + file LICENSE NA NA NA NA no 3.6.2
crrstep crrstep /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2015-2.1 NA cmprsk NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
crul crul /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9.0 NA NA curl (>= 3.3), R6 (>= 2.2.0), urltools (>= 1.6.0), httpcode (>= 0.2.0), jsonlite, mime NA testthat, fauxpas (>= 0.1.0), webmockr (>= 0.1.0), knitr NA MIT + file LICENSE NA NA NA NA no 3.6.1
cubature cubature /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.4 NA NA Rcpp Rcpp testthat, knitr, mvtnorm, benchr NA GPL-3 NA NA NA NA yes 3.6.1
Cubist Cubist /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.3 NA lattice reshape2, utils NA mlbench, caret, knitr, modeldata, dplyr (>= 0.7.4), rlang, tidyrules NA GPL-3 NA NA NA NA yes 3.6.1
curl curl /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.3 NA R (>= 3.0.0) NA NA spelling, testthat (>= 1.0.0), knitr, jsonlite, rmarkdown, magrittr, httpuv (>= 1.4.4), webutils NA MIT + file LICENSE NA NA NA NA yes 3.6.1
cutpointr cutpointr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.2 NA R (>= 3.5.0) gridExtra (>= 2.2.1), foreach (>= 1.4.3), dplyr (>= 0.8.0), tidyr (>= 1.0.0), purrr (>= 0.3.0), tibble (>= 3.0.0), ggplot2 (>= 3.0.0), Rcpp (>= 0.12.12), stats, utils, rlang (>= 0.4.0) Rcpp KernSmooth (>= 2.23-15), fANCOVA (>= 0.5-1), testthat (>= 1.0.2), doRNG (>= 1.6), doParallel (>= 1.0.11), knitr, rmarkdown, mgcv (>= 1.8), crayon (>= 1.3.4), registry (>= 0.5-1), pkgmaker(>= 0.31.1), NA GPL-3 NA NA NA NA yes 3.6.2
cyclocomp cyclocomp /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA NA callr, crayon, desc, remotes, withr NA testthat NA MIT + file LICENSE NA NA NA NA no 3.6.1
d3heatmap d3heatmap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.1.2 NA NA scales (>= 0.2.5), htmlwidgets, png, base64enc, dendextend (>= 0.18.0), stats, grDevices NA shiny, knitr, rmarkdown NA GPL-3 | file LICENSE NA NA NA NA no 3.6.1
data.table data.table /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.12.8 NA R (>= 3.1.0) methods NA bit64, curl, R.utils, knitr, xts, nanotime, zoo, yaml NA MPL-2.0 | file LICENSE NA NA NA NA yes 3.6.2
DBI DBI /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA methods, R (>= 3.0.0) NA NA blob, covr, hms, knitr, magrittr, rmarkdown, rprojroot, RSQLite (>= 1.1-2), testthat, xml2 NA LGPL (>= 2.1) NA NA NA NA no 3.6.1
dbplyr dbplyr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.3 NA R (>= 3.1) assertthat (>= 0.2.0), DBI (>= 1.0.0), dplyr (>= 0.8.0), glue (>= 1.2.0), lifecycle, methods, purrr (>= 0.2.5), R6 (>= 2.2.2), rlang (>= 0.2.0), tibble (>= 1.4.2), tidyselect (>= 0.2.4), utils NA bit64, covr, knitr, Lahman, nycflights13, RMariaDB (>= 1.0.2), rmarkdown, RPostgres (>= 1.1.3), RSQLite (>= 2.1.0), testthat (>= 2.0.0) NA MIT + file LICENSE NA NA NA NA no 3.6.2
dbscan dbscan /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-5 NA NA Rcpp (>= 1.0.0), graphics, stats, methods Rcpp fpc, microbenchmark, testthat, dendextend, igraph, knitr, DMwR NA GPL (>= 2) NA NA NA NA yes 3.6.1
deepnet deepnet /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2 NA NA NA NA NA NA GPL NA NA NA NA no 3.6.2
DelayedArray DelayedArray /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.10.0 NA R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.27.1), S4Vectors (>= 0.21.7), IRanges (>= 2.17.3), BiocParallel stats, Matrix S4Vectors Matrix, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit NA Artistic-2.0 NA NA NA NA yes 3.6.0
DelayedMatrixStats DelayedMatrixStats /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.1 NA DelayedArray (>= 0.9.8) methods, matrixStats (>= 0.55.0), Matrix, S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.7.10), BiocParallel NA testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem NA MIT + file LICENSE NA NA NA NA no 3.6.1
dendextend dendextend /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.13.4 NA R (>= 3.0.0) utils, stats, datasets, magrittr (>= 1.0.1), ggplot2, viridis NA knitr, rmarkdown, testthat, seriation, colorspace, ape, microbenchmark, gplots, heatmaply, d3heatmap, dynamicTreeCut, pvclust, corrplot, DendSer, MASS, cluster, fpc, circlize (>= 0.2.5), covr ggdendro, dendroextras, Hmisc, data.table, rpart GPL-2 | GPL-3 NA NA NA NA no 3.6.2
DendSer DendSer /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA gclus,seriation NA NA NA NA GPL-2 NA NA NA NA yes 3.6.1
DEoptimR DEoptimR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-8 NA NA stats NA NA robustbase GPL (>= 2) NA NA NA NA no 3.6.1
Deriv Deriv /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.0 NA NA methods NA testthat NA GPL (>= 3) NA NA NA NA no 3.6.1
desc desc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.0 NA R (>= 3.1.0) assertthat, utils, R6, crayon, rprojroot NA covr, testthat, whoami, withr NA MIT + file LICENSE NA NA NA NA no 3.6.0
descr descr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.4 NA NA xtable, utils, grDevices, graphics, stats NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
DESeq DESeq /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.36.0 NA BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice genefilter, geneplotter, methods, MASS, RColorBrewer NA pasilla (>= 0.2.10), vsn, gplots NA GPL (>= 3) NA NA NA NA yes 3.6.1
DESeq2 DESeq2 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.24.0 NA S4Vectors (>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0) Rcpp, RcppArmadillo testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10) NA LGPL (>= 3) NA NA NA NA yes 3.6.0
desirability desirability /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1 NA NA stats, graphics, grDevices NA lattice NA GPL-2 NA NA NA NA no 3.6.1
devtools devtools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3.0 NA R (>= 3.0.2), usethis (>= 1.6.0) callr (>= 3.4.3), cli (>= 2.0.2), covr (>= 3.5.0), crayon (>= 1.3.4), desc (>= 1.2.0), digest (>= 0.6.25), DT (>= 0.13), ellipsis (>= 0.3.0), glue (>= 1.4.0), git2r (>= 0.26.1), httr (>= 1.4.1), jsonlite (>= 1.6.1), memoise (>= 1.1.0), pkgbuild (>= 1.0.6), pkgload (>= 1.0.2), rcmdcheck (>= 1.3.3), remotes (>= 2.1.1), rlang (>= 0.4.5), roxygen2 (>= 7.1.0), rstudioapi (>= 0.11), rversions (>= 2.0.1), sessioninfo (>= 1.1.1), stats, testthat (>= 2.3.2), tools, utils, withr (>= 2.1.2) NA BiocManager (>= 1.30.10), curl (>= 4.3), foghorn (>= 1.1.5), gmailr (>= 1.0.0), knitr (>= 1.28), lintr (>= 2.0.1), mockery (>= 0.4.2), pingr (>= 2.0.0), MASS, pkgdown (>= 1.5.1), rhub (>= 1.1.1), rmarkdown (>= 2.1), spelling (>= 2.1) NA GPL (>= 2) NA NA NA NA no 3.6.2
DiagrammeR DiagrammeR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.6.1 NA R (>= 3.2.0) dplyr (>= 0.7.6), downloader (>= 0.4), glue (>= 1.3.0), htmltools (>= 0.3.6), htmlwidgets (>= 1.2), igraph (>= 1.2.2), influenceR (>= 0.1.0), magrittr (>= 1.5), purrr (>= 0.2.5), RColorBrewer (>= 1.1-2), readr (>= 1.1.1), rlang (>= 0.2.2), rstudioapi (>= 0.7), scales (>= 1.0.0), stringr (>= 1.3.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), viridis (>= 0.5.1), visNetwork (>= 2.0.4) NA covr, DiagrammeRsvg, rsvg, knitr, testthat, rmarkdown NA MIT + file LICENSE NA NA NA NA no 3.6.2
diffobj diffobj /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA R (>= 3.1.0) crayon (>= 1.3.2), tools, methods, utils, stats NA knitr, rmarkdown, testthat NA GPL (>= 2) NA NA NA NA yes 3.6.2
digest digest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.25 NA R (>= 3.1.0) utils NA tinytest, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 3.6.2
diptest diptest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.75-7 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
DMwR DMwR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.1 NA R(>= 2.10), methods, graphics, lattice (>= 0.18-3), grid (>= 2.10.1) xts (>= 0.6-7), quantmod (>= 0.3-8), zoo (>= 1.6-4), abind (>= 1.1-0), rpart (>= 3.1-46), class (>= 7.3-1), ROCR (>= 1.0) NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
DO.db DO.db /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.9 NA R (>= 2.7.0), methods, AnnotationDbi (>= 1.9.7) methods, AnnotationDbi NA NA NA Artistic-2.0 NA NA NA NA no 3.6.1
doBy doBy /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.6.5 NA R (>= 3.6.0), methods pbkrtest (>= 0.4-8.1), MASS, Matrix, dplyr, plyr, magrittr, Deriv, tibble, broom NA multcomp, geepack, lme4, survival, ggplot2, knitr NA GPL (>= 2) NA NA NA NA no 3.6.2
docker4seq docker4seq /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3.4 NA R (>= 3.0.0) NA NA BiocStyle, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 3.6.1
doParallel doParallel /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.15 NA R (>= 2.14.0), foreach(>= 1.2.0), iterators(>= 1.0.0), parallel, utils NA NA caret, mlbench, rpart, RUnit compiler GPL-2 NA NA NA NA no 3.6.2
doRNG doRNG /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.8.2 NA R (>= 3.0.0), foreach, rngtools (>= 1.5) stats, utils, iterators NA doParallel, doMPI, doRedis, rbenchmark, devtools, knitr, bibtex, testthat, pkgmaker (>= 0.31) NA GPL (>= 2) NA NA NA NA no 3.6.2
DOSE DOSE /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.10.2 NA R (>= 3.4.0) AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim (>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils NA prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat NA Artistic-2.0 NA NA NA NA no 3.6.1
doParallel doParallel /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.18 NA R (>= 2.5.0), foreach(>= 1.2.0), iterators(>= 1.0.0), snow(>= 0.3.0), utils NA NA compiler, RUnit, caret, mlbench, rpart, parallel NA GPL-2 NA NA NA NA no 3.6.2
dotCall64 dotCall64 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-0 NA R (>= 3.1) NA NA microbenchmark, OpenMPController, RColorBrewer, roxygen2, spam, testthat, NA GPL (>= 2) NA NA NA NA yes 3.6.1
downloader downloader /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4 NA NA utils, digest NA testthat NA GPL-2 NA NA NA NA no 3.6.1
dplyr dplyr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.8.5 NA R (>= 3.2.0) ellipsis, assertthat (>= 0.2.0), glue (>= 1.3.0), magrittr (>= 1.5), methods, pkgconfig, R6, Rcpp (>= 1.0.1), rlang (>= 0.4.0), tibble (>= 2.0.0), tidyselect (>= 0.2.5), utils BH, plogr (>= 0.2.0), Rcpp (>= 1.0.1) bit64, callr, covr, crayon (>= 1.3.4), DBI, dbplyr, dtplyr, ggplot2, hms, knitr, Lahman, lubridate, MASS, mgcv, microbenchmark, nycflights13, rmarkdown, RMySQL, RPostgreSQL, RSQLite, testthat, withr, broom, purrr, readr NA MIT + file LICENSE NA NA NA NA yes 3.6.2
DT DT /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.13 NA NA htmltools (>= 0.3.6), htmlwidgets (>= 1.3), jsonlite (>= 0.9.16), magrittr, crosstalk, promises NA knitr (>= 1.8), rmarkdown, shiny (>= 1.2.0) NA GPL-3 | file LICENSE NA NA NA NA no 3.6.2
dtplyr dtplyr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA R (>= 3.2) crayon, data.table (>= 1.12.4), dplyr (>= 0.8.1), rlang, tibble, tidyselect NA bench, covr, knitr, rmarkdown, testthat (>= 2.1.0) NA GPL-3 NA NA NA NA no 3.6.2
dtw dtw /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.21-3 NA R (>= 2.10.0), proxy graphics, grDevices, stats, utils NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
dynamicTreeCut dynamicTreeCut /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.63-1 NA R (>= 2.3.0), stats NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
DynNom DynNom /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.0.1 NA magrittr survival (>= 2.38-3), shiny, ggplot2 (> 2.1.0), plotly, stargazer, prediction, rms, dplyr, compare, BBmisc NA gam, mgcv NA GPL-2 NA NA NA NA no 3.6.1
e1071 e1071 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7-3 NA NA graphics, grDevices, class, stats, methods, utils NA cluster, mlbench, nnet, randomForest, rpart, SparseM, xtable, Matrix, MASS, slam NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
earth earth /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.1.2 NA R (>= 3.4.0), Formula (>= 1.2-3), plotmo (>= 3.5.4), TeachingDemos (>= 2.10) NA NA gam (>= 1.16), mgcv (>= 1.8-26), mda (>= 0.4-10), MASS (>= 7.3-51) NA GPL-3 NA NA NA NA yes 3.6.1
EDASeq EDASeq /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.18.0 NA Biobase (>= 2.15.1), ShortRead (>= 1.11.42) methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq, aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager NA BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat NA Artistic-2.0 NA NA NA NA no 3.6.1
edgeR edgeR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.26.8 NA R (>= 3.6.0), limma (>= 3.34.5) graphics, stats, utils, methods, locfit, Rcpp Rcpp AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines NA GPL (>=2) NA NA NA NA yes 3.6.2
egg egg /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.5 NA gridExtra (>= 2.3), ggplot2 gtable, grid, grDevices, utils NA knitr, png NA GPL-3 NA NA NA NA no 3.6.1
ellipse ellipse /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.1 NA R (>= 2.0.0),graphics,stats NA NA MASS NA GPL (>= 2) NA NA NA NA no 3.6.1
ellipsis ellipsis /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA R (>= 3.2) rlang (>= 0.3.0) NA covr, testthat NA GPL-3 NA NA NA NA yes 3.6.1
emdbook emdbook /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.12 NA NA MASS, lattice, plyr, coda, bbmle NA R2jags, ellipse, SuppDists, numDeriv, testthat, rgl NA GPL NA NA NA NA no 3.6.2
enc enc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.2 NA R (>= 3.1) methods NA digest, pillar, readr, rlang, testthat, withr NA GPL-3 NA NA NA NA yes 3.6.2
EnhancedVolcano EnhancedVolcano /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.5 NA ggplot2, ggrepel NA RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, gridExtra, magrittr NA GPL-3 NA NA NA NA no 3.6.1
enrichplot enrichplot /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.0 NA R (>= 3.4.0) AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2, ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices, grid, gridExtra, igraph, methods, purrr, RColorBrewer, reshape2, stats, UpSetR, utils NA clusterProfiler, dplyr, knitr, org.Hs.eg.db, prettydoc NA Artistic-2.0 NA NA NA NA no 3.6.1
entropy entropy /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.1 NA R (>= 2.15.1) NA NA NA GPL (>= 3) NA NA NA NA no 3.6.1
epiDisplay epiDisplay /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.5.0.1 NA R (>= 2.6.2), foreign, survival, MASS, nnet NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
europepmc europepmc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3 NA R (>= 3.00) httr, jsonlite, plyr, dplyr, progress, urltools, purrr, xml2 NA testthat, knitr, rmarkdown, ggplot2, readr NA GPL-3 NA NA NA NA no 3.6.1
evaluate evaluate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.14 NA R (>= 3.0.2) methods NA testthat, lattice, ggplot2 NA MIT + file LICENSE NA NA NA NA no 3.6.0
evtree evtree /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-8 NA R (>= 3.3.0), partykit NA NA Formula, kernlab, lattice, mlbench, multcomp, party, rpart, xtable NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.0
exactRankTests exactRankTests /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.8-31 NA R (>= 2.4.0), stats, utils NA NA survival NA GPL (>= 2) NA NA NA NA yes 3.6.1
ezfun ezfun /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.3 NA R (>= 3.1.0) NA NA knitr, rmarkdown NA GPL-2 NA NA NA NA no 3.6.2
factoextra factoextra /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.7 NA R (>= 3.1.2), ggplot2 (>= 2.2.0) abind, cluster, dendextend, FactoMineR, ggpubr(>= 0.1.5), grid, stats, reshape2, ggrepel, tidyr NA ade4, ca, igraph, MASS, knitr, mclust NA GPL-2 NA NA NA NA no 3.6.2
FactoMineR FactoMineR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3 NA R (>= 3.5.0) car,cluster,ellipse,flashClust,graphics,grDevices,lattice,leaps,MASS,scatterplot3d,stats,utils,ggplot2,ggrepel NA missMDA,knitr,Factoshiny NA GPL (>= 2) NA NA NA NA no 3.6.2
fansi fansi /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.1 NA R (>= 3.1.0) NA NA unitizer, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 3.6.1
farver farver /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.3 NA NA NA NA testthat (>= 2.1.0), covr NA MIT + file LICENSE NA NA NA NA yes 3.6.1
fastICA fastICA /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2-2 NA R (>= 3.0.0) NA NA MASS NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
fastmap fastmap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA NA NA NA testthat (>= 2.1.1) NA MIT + file LICENSE NA NA NA NA yes 3.6.1
fastmatch fastmatch /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-0 NA NA NA NA NA NA GPL-2 NA NA NA NA yes 3.6.1
fBasics fBasics /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3042.89.1 NA R (>= 2.15.1), timeDate, timeSeries stats, grDevices, graphics, methods, utils, MASS, spatial, gss, stabledist NA akima, RUnit, tcltk NA GPL (>= 2) NA NA NA NA yes 3.6.2
fgsea fgsea /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.10.1 NA R (>= 3.3), Rcpp data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), gridExtra, grid, fastmatch, Matrix, utils Rcpp, BH testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery NA MIT + file LICENCE NA NA NA NA yes 3.6.1
fields fields /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 10.3 NA R (>= 3.0), methods, spam, maps NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.2
flashClust flashClust /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.01-2 NA R (>= 2.3.0) NA NA NA NA GPL (>= 2) NA NA NA NA NA 3.6.1
flexclust flexclust /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-0 NA R (>= 2.14.0), graphics, grid, lattice, modeltools methods, parallel, stats, stats4, class NA ellipse, clue, cluster, seriation, skmeans NA GPL-2 NA NA NA NA yes 3.6.1
flexmix flexmix /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3-15 NA R (>= 2.15.0), lattice graphics, grid, grDevices, methods, modeltools (>= 0.2-16), nnet, stats, stats4, utils NA actuar, codetools, diptest, Ecdat, ellipse, gclus, glmnet, lme4 (>= 1.1), MASS, mgcv (>= 1.8-0), mlbench, multcomp, mvtnorm, SuppDists, survival NA GPL (>= 2) NA NA NA NA no 3.6.1
FNN FNN /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.3 NA R (>= 3.0.0) NA NA chemometrics, mvtnorm NA GPL (>= 2) NA NA NA NA yes 3.6.1
foghorn foghorn /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.1 NA R (>= 3.1.0) clisymbols (>= 1.0.0), crayon (>= 1.3.2), curl (>= 2.2), httr (>= 1.2.1), jsonlite (>= 1.5), rlang (>= 0.4.3), rvest (>= 0.3.2), tibble (>= 1.2), xml2 (>= 1.0.0) NA covr, dplyr, knitr, progress, rmarkdown, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.2
fontBitstreamVera fontBitstreamVera /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.1 NA R (>= 3.0.0) NA NA NA NA file LICENCE yes NA NA NA no 3.6.1
fontLiberation fontLiberation /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.0 NA R (>= 3.0) NA NA NA NA file LICENSE yes NA NA NA no 3.6.1
fontquiver fontquiver /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.1 NA R (>= 3.0.0) fontBitstreamVera (>= 0.1.0), fontLiberation (>= 0.1.0) NA testthat, htmltools NA GPL-3 | file LICENSE NA NA NA NA no 3.6.1
forcats forcats /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.0 NA R (>= 3.2) ellipsis, magrittr, rlang, tibble NA covr, ggplot2, testthat, readr, knitr, rmarkdown, dplyr NA GPL-3 NA NA NA NA no 3.6.2
foreach foreach /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5.0 NA R (>= 2.5.0) codetools, utils, iterators NA randomForest, doMC, doParallel, testthat, knitr, rmarkdown NA Apache License (== 2.0) NA NA NA NA no 3.6.2
formatR formatR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7 NA R (>= 3.0.2) NA NA codetools, shiny, testit, rmarkdown, knitr NA GPL NA NA NA NA no 3.6.0
Formula Formula /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2-3 NA R (>= 2.0.0), stats NA NA NA NA GPL-2 | GPL-3 NA NA NA NA no 3.6.0
fpc fpc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2-5 NA R (>= 2.0) MASS, cluster, mclust, flexmix, prabclus, class, diptest, robustbase, kernlab, grDevices, graphics, methods, stats, utils, parallel NA tclust, pdfCluster, EMMIXskew, mvtnorm NA GPL NA NA NA NA no 3.6.2
freetypeharfbuzz freetypeharfbuzz /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.5 NA R (>= 3.2) fontquiver NA covr, testthat NA GPL-3 | file LICENSE NA NA NA NA yes 3.6.1
fs fs /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.1 NA R (>= 3.1) methods NA testthat, covr, pillar (>= 1.0.0), tibble (>= 1.1.0), crayon, rmarkdown, knitr, withr, spelling NA GPL-3 NA NA NA NA yes 3.6.2
FSelector FSelector /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.31 NA NA randomForest, RWeka, digest, entropy NA mlbench, rpart NA GPL-2 NA NA NA NA no 3.6.1
funModeling funModeling /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.9.3 NA R (>= 3.4.0), Hmisc (>= 3.17.1) ROCR, ggplot2, gridExtra, pander, reshape2, scales, dplyr, lazyeval, utils, RColorBrewer, moments, entropy, cli, stringr NA knitr, rmarkdown NA GPL-2 NA NA NA NA no 3.6.1
furrr furrr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.0 NA R (>= 3.2.0), future (>= 1.6.2) globals (>= 0.10.3), rlang (>= 0.2.0), purrr (>= 0.2.4) NA listenv (>= 0.6.0), dplyr (>= 0.7.4), testthat NA LGPL (>= 2.1) NA NA NA NA no 3.6.1
futile.logger futile.logger /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.3 NA R (>= 3.0.0) utils, lambda.r (>= 1.1.0), futile.options NA testthat, jsonlite NA LGPL-3 NA NA NA NA no 3.6.0
futile.options futile.options /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA R (>= 2.8.0) NA NA NA NA LGPL-3 NA NA NA NA no 3.6.0
future future /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.17.0 NA NA digest, globals (>= 0.12.5), listenv (>= 0.8.0), parallel, utils NA RhpcBLASctl, R.rsp, markdown NA LGPL (>= 2.1) NA NA NA NA no 3.6.2
GA GA /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.2.1 NA R (>= 3.4), methods, foreach, iterators stats, graphics, grDevices, utils, cli, crayon, Rcpp Rcpp, RcppArmadillo parallel, doParallel, doRNG (>= 1.6), knitr (>= 1.8) NA GPL (>= 2) NA NA NA NA yes 3.6.1
gam gam /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.16.1 NA stats, splines, foreach NA NA akima NA GPL-2 NA NA NA NA yes 3.6.1
gargle gargle /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.0 NA R (>= 3.2) fs (>= 1.3.1), glue (>= 1.3.0), httr (>= 1.4.0), jsonlite, rlang (>= 0.4.2), stats, withr NA covr, knitr, rmarkdown, sodium, spelling, testthat (>= 2.3.2) NA MIT + file LICENSE NA NA NA NA no 3.6.2
gbm gbm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1.5 NA R (>= 2.9.0) gridExtra, lattice, parallel, survival NA knitr, pdp, RUnit, splines, viridis NA GPL (>= 2) | file LICENSE NA NA NA NA yes 3.6.0
gclus gclus /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.2 NA R (>= 2.10), cluster NA NA knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 3.6.1
gdata gdata /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.18.0 NA R (>= 2.3.0) gtools, stats, methods, utils NA RUnit NA GPL-2 NA NA NA NA no 3.6.0
GDCRNATools GDCRNATools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.1 NA R (>= 3.5.0) shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel NA knitr, testthat NA Artistic-2.0 NA NA NA NA no 3.6.2
gdtools gdtools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.2 NA NA Rcpp (>= 0.12.12), systemfonts (>= 0.1.1) Rcpp htmltools, testthat, fontquiver (>= 0.2.0), curl NA GPL-3 | file LICENSE NA NA NA NA yes 3.6.2
geepack geepack /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-1 NA R (>= 3.5.0), methods MASS, broom, magrittr NA NA NA GPL (>= 3) NA NA NA NA yes 3.6.1
genefilter genefilter /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.66.0 NA NA S4Vectors (>= 0.9.42), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival NA class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr NA Artistic-2.0 NA NA NA NA yes 3.6.0
geneplotter geneplotter /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.62.0 NA R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils NA Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db NA Artistic-2.0 NA NA NA NA no 3.6.0
generics generics /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0.2 NA R (>= 3.1) methods NA covr, pkgload, testthat, tibble NA GPL-2 NA NA NA NA no 3.6.0
genetics genetics /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.8.1.2 NA combinat, gdata, gtools, MASS, mvtnorm NA NA NA NA GPL NA NA NA NA no 3.6.0
GenomeInfoDb GenomeInfoDb /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.20.0 NA R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12) stats, stats4, utils, RCurl, GenomeInfoDbData NA GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr NA Artistic-2.0 NA NA NA NA no 3.6.0
GenomeInfoDbData GenomeInfoDbData /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.1 NA R (>= 3.5.0) NA NA NA NA Artistic-2.0 NA NA NA NA no 3.6.0
GenomicAlignments GenomicAlignments /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.20.1 NA R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.19.11), IRanges (>= 2.15.12), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.33.4), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2) methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel S4Vectors, IRanges ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle NA Artistic-2.0 NA NA NA NA yes 3.6.1
GenomicDataCommons GenomicDataCommons /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.8.0 NA R (>= 3.4.0), magrittr stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment, S4Vectors, tibble NA BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools NA Artistic-2.0 NA NA NA NA no 3.6.1
GenomicFeatures GenomicFeatures /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.36.4 NA BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.15.4), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4) methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector (>= 0.19.7), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7), biomaRt (>= 2.17.1), Biobase (>= 2.15.1) NA RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr NA Artistic-2.0 NA NA NA NA no 3.6.1
GenomicRanges GenomicRanges /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.36.1 NA R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.19.11), IRanges (>= 2.17.1), GenomeInfoDb (>= 1.15.2) utils, stats, XVector (>= 0.19.8) S4Vectors, IRanges Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle NA Artistic-2.0 NA NA NA NA yes 3.6.1
GetoptLong GetoptLong /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.8 NA R (>= 3.0.0) rjson, GlobalOptions (>= 0.1.0), methods NA testthat (>= 1.0.0), knitr, markdown NA MIT + file LICENSE NA NA NA NA no 3.6.1
GGally GGally /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5.0 NA R (>= 3.1), ggplot2 (> 2.2.0) grDevices, grid, gtable (>= 0.2.0), plyr (>= 1.8.3), progress, RColorBrewer, reshape (>= 0.8.5), utils, rlang NA broom (>= 0.4.0), chemometrics, geosphere (>= 1.5-1), igraph (>= 1.0.1), intergraph (>= 2.0-2), maps (>= 3.1.0), mapproj, network (>= 1.12.0), scagnostics, scales (>= 0.4.0), sna (>= 2.3-2), survival, packagedocs (>= 0.4.0), rmarkdown, roxygen2, testthat, crosstalk NA GPL (>= 2.0) NA NA NA NA no 3.6.2
ggbeeswarm ggbeeswarm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.0 NA R (>= 3.0.0), ggplot2 (>= 2.0) beeswarm, vipor NA gridExtra NA GPL (>= 2) NA NA NA NA no 3.6.0
ggbiplot ggbiplot /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.55 NA ggplot2, plyr, scales, grid NA NA NA NA GPL-2 NA NA NA NA no 3.6.1
ggdendro ggdendro /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-20 NA NA MASS, ggplot2(>= 0.9.2) NA rpart(>= 4.0-0), tree, testthat, knitr, cluster, scales NA GPL-2 | GPL-3 NA NA NA NA no 3.6.1
ggforce ggforce /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.1 NA ggplot2 (>= 3.0.0), R (>= 3.3.0) Rcpp (>= 0.12.2), grid, scales, MASS, tweenr (>= 0.1.5), gtable, rlang, polyclip, stats, grDevices, tidyselect, withr, utils Rcpp, RcppEigen sessioninfo, concaveman, deldir, reshape2, units (>= 0.4-6) NA MIT + file LICENSE NA NA NA NA yes 3.6.1
ggplot2 ggplot2 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.3.0 NA R (>= 3.2) digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband, MASS, mgcv, rlang (>= 0.3.0), scales (>= 0.5.0), stats, tibble, withr (>= 2.0.0) NA covr, dplyr, ggplot2movies, hexbin, Hmisc, knitr, lattice, mapproj, maps, maptools, multcomp, munsell, nlme, profvis, quantreg, rgeos, rmarkdown, rpart, sf (>= 0.7-3), svglite (>= 1.2.0.9001), testthat (>= 2.1.0), vdiffr (>= 0.3.0) sp GPL-2 | file LICENSE NA NA NA NA no 3.6.2
ggplot2movies ggplot2movies /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0.1 NA R (>= 2.10.0) NA NA NA NA GPL-3 NA NA NA NA no 3.6.1
ggplotify ggplotify /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0.5 NA R (>= 3.4.0) ggplot2, graphics, grDevices, grid, gridGraphics, rvcheck NA colorspace, cowplot, ggimage, knitr, lattice, prettydoc, vcd NA Artistic-2.0 NA NA NA NA no 3.6.2
ggpubr ggpubr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA R (>= 3.1.0), ggplot2 ggrepel, grid, ggsci, stats, utils, tidyr, purrr, dplyr (>= 0.7.1), cowplot, ggsignif, scales, gridExtra, glue, polynom, rlang, rstatix (>= 0.4.0), tibble, magrittr NA grDevices, knitr, RColorBrewer, gtable NA GPL-2 NA NA NA NA no 3.6.2
ggraph ggraph /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.2 NA R (>= 2.10), ggplot2 (>= 3.0.0) Rcpp (>= 0.12.2), dplyr, ggforce (>= 0.3.1), grid, igraph (>= 1.0.0), scales, MASS, digest, gtable, ggrepel, utils, stats, viridis, rlang, tidygraph, graphlayouts (>= 0.5.0) Rcpp network, knitr, rmarkdown, purrr, tibble, seriation, deldir, gganimate NA MIT + file LICENSE NA NA NA NA yes 3.6.2
ggraptR ggraptR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2 NA dplyr (>= 0.7.5), ggplot2 (>= 2.2.0), pacman (>= 0.4.6), purrr(>= 0.2.4), shiny (>= 0.12.2) NA NA knitr NA GPL (>= 2) NA NA NA NA no 3.6.1
ggrepel ggrepel /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.8.2 NA R (>= 3.0.0), ggplot2 (>= 2.2.0) grid, Rcpp, scales (>= 0.3.0) Rcpp knitr, rmarkdown, testthat, gridExtra, devtools, prettydoc NA GPL-3 | file LICENSE NA NA NA NA yes 3.6.2
ggridges ggridges /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.2 NA R (>= 3.2) ggplot2 (>= 3.0.0), grid (>= 3.0.0), plyr (>= 1.8.0), scales (>= 0.4.1), withr (>= 2.1.1) NA covr, dplyr, patchwork, ggplot2movies, forcats, knitr, rmarkdown, testthat, vdiffr NA GPL-2 | file LICENSE NA NA NA NA no 3.6.1
ggsci ggsci /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.9 NA R (>= 3.0.2) grDevices, scales, ggplot2 (>= 2.0.0) NA knitr, rmarkdown, gridExtra, reshape2 NA GPL-3 | file LICENSE NA NA NA NA no 3.6.0
ggsignif ggsignif /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.0 NA NA ggplot2 (>= 2.0.0) NA testthat, knitr, rmarkdown NA GPL-3 NA NA NA NA no 3.6.1
ggthemes ggthemes /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.2.0 NA R (>= 3.3.0) ggplot2 (>= 3.0.0), graphics, grid, methods, purrr, scales, stringr, tibble NA dplyr, covr, extrafont, glue, knitr, lattice, lintr, maps, mapproj, pander, rlang, rmarkdown, spelling, testthat, tidyr, vdiffr, withr NA GPL-2 NA NA NA NA no 3.6.1
gh gh /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA NA cli, ini, jsonlite, httr (>= 1.2) NA covr, keyring, pingr, testthat, withr NA MIT + file LICENSE NA NA NA NA no 3.6.2
git2r git2r /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.27.1 NA R (>= 3.1) graphics, utils NA getPass NA GPL-2 NA NA NA NA yes 3.6.2
gld gld /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.6.2 NA NA stats, graphics, e1071, lmom NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
glmnet glmnet /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0-2 NA R (>= 3.6.0), Matrix (>= 1.0-6) methods, utils, foreach, shape NA survival, knitr, lars NA GPL-2 NA NA NA NA yes 3.6.1
GlobalOptions GlobalOptions /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.1 NA R (>= 3.3.0), methods utils NA testthat (>= 1.0.0), knitr, markdown NA MIT + file LICENSE NA NA NA NA no 3.6.1
globals globals /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.12.5 NA R (>= 3.1.2) codetools NA NA NA LGPL (>= 2.1) NA NA NA NA no 3.6.1
glue glue /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.0 NA R (>= 3.1) methods NA testthat, covr, magrittr, crayon, knitr, rmarkdown, DBI, RSQLite, R.utils, forcats, microbenchmark, rprintf, stringr, ggplot2, dplyr, withr, vctrs (>= 0.2.2) NA MIT + file LICENSE NA NA NA NA yes 3.6.2
gmailr gmailr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA R (>= 3.0.0) base64enc, crayon, gargle, httr, jsonlite, lifecycle, magrittr, mime, rematch2 NA covr, knitr, methods, sodium, rmarkdown, testthat, xml2 NA MIT + file LICENSE NA NA NA NA no 3.6.1
GO.db GO.db /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.8.2 NA R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1) methods, AnnotationDbi NA DBI NA Artistic-2.0 NA NA NA NA no 3.6.1
goftest goftest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2-2 NA R (>= 3.3) stats NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.2
GOSemSim GOSemSim /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.10.0 NA R (>= 3.4.0) AnnotationDbi, GO.db, methods, utils Rcpp AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat NA Artistic-2.0 NA NA NA NA yes 3.6.1
gower gower /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.1 NA NA NA NA tinytest (>= 0.9.3), NA GPL-3 NA NA NA NA yes 3.6.0
gplots gplots /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0.3 NA R (>= 3.0) gtools, gdata, stats, caTools, KernSmooth NA grid, MASS, knitr NA GPL-2 NA NA NA NA no 3.6.2
gpuR gpuR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.3 NA R (>= 3.0.2), methods, utils Rcpp (>= 0.12.15), assertive Rcpp (>= 0.12.15), RcppEigen (>= 0.3.3.4.0), RViennaCL (>= 1.7.1.7), BH testthat, knitr NA GPL (>= 2) NA NA NA NA yes 3.6.1
graph graph /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.62.0 NA R (>= 2.10), methods, BiocGenerics (>= 0.13.11) stats, stats4, utils NA SparseM (>= 0.36), XML, RBGL, RUnit, cluster Rgraphviz Artistic-2.0 NA NA NA NA yes 3.6.1
graphlayouts graphlayouts /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7.0 NA R (>= 3.2.0) igraph, Rcpp Rcpp, RcppArmadillo oaqc, testthat, ggraph, ggplot2, knitr, rmarkdown NA MIT + file LICENSE NA NA NA NA yes 3.6.2
gridExtra gridExtra /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3 NA NA gtable, grid, grDevices, graphics, utils NA ggplot2, egg, lattice, knitr, testthat NA GPL (>= 2) NA NA NA NA no 3.6.2
gridGraphics gridGraphics /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5-0 NA grid, graphics grDevices NA magick (>= 1.3), pdftools (>= 1.6) NA GPL (>= 2) NA NA NA NA no 3.6.2
gss gss /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2-0 NA R (>= 3.0.0), stats NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.2
gsubfn gsubfn /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7 NA proto NA NA boot, chron, grid, lattice, quantreg, svUnit, tcltk, zoo NA GPL (>= 2) NA NA NA NA no 3.6.1
gtable gtable /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA R (>= 3.0) grid NA covr, testthat, knitr, rmarkdown, ggplot2, profvis NA GPL-2 NA NA NA NA no 3.6.0
gtools gtools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.8.2 NA methods, stats, utils NA NA NA NA GPL-2 NA NA NA NA yes 3.6.2
gWidgets gWidgets /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-54.2 NA methods, utils NA NA gWidgetstcltk NA GPL (>= 2) NA NA NA NA no 3.6.2
haven haven /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2.0 NA R (>= 3.2) forcats (>= 0.2.0), hms, Rcpp (>= 0.11.4), readr (>= 0.1.0), rlang (>= 0.4.0), tibble, tidyselect Rcpp covr, fs, knitr, rmarkdown, testthat, pillar (>= 1.4.0), cli, crayon NA MIT + file LICENSE NA NA NA NA yes 3.6.1
HDF5Array HDF5Array /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.12.3 NA R (>= 3.4), methods, DelayedArray (>= 0.9.3), rhdf5 (>= 2.25.6) utils, tools, BiocGenerics (>= 0.25.1), S4Vectors, IRanges S4Vectors (>= 0.21.6), Rhdf5lib h5vcData, SummarizedExperiment (>= 1.9.6), GenomicRanges, ExperimentHub, TENxBrainData, BiocParallel, GenomicFeatures, BiocStyle NA Artistic-2.0 NA NA NA NA yes 3.6.1
heatmaply heatmaply /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA R (>= 3.0.0), plotly (>= 4.7.1), viridis ggplot2 (>= 2.2.0), dendextend (>= 1.12.0), magrittr (>= 1.0.1), reshape2, scales, seriation, utils, stats, grDevices, methods, colorspace, RColorBrewer, htmlwidgets, webshot, assertthat, egg NA knitr, covr, gplots, tidyselect, rmarkdown, testthat NA GPL-2 | GPL-3 NA NA NA NA no 3.6.2
hexbin hexbin /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.28.1 NA R (>= 2.0.1), methods lattice, grid, graphics, grDevices, stats, utils NA marray, affy, Biobase, limma, knitr NA GPL-2 NA NA NA NA yes 3.6.2
highlight highlight /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.0 NA R (>= 3.2) grDevices, tools NA NA NA GPL (>= 3) NA NA NA NA yes 3.6.1
highr highr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.8 NA R (>= 3.2.3) NA NA knitr, testit NA GPL NA NA NA NA no 3.6.0
hmeasure hmeasure /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-2 NA R (>= 2.10) NA NA MASS, class, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.1
Hmisc Hmisc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.4-0 NA lattice, survival (>= 3.1-6), Formula, ggplot2 (>= 2.2) methods, latticeExtra, cluster, rpart, nnet, acepack, foreign, gtable, grid, gridExtra, data.table, htmlTable (>= 1.11.0), viridis, htmltools, base64enc NA chron, rms, mice, tables, knitr, ff, ffbase, plotly (>= 4.5.6), rlang NA GPL (>= 2) NA NA NA NA yes 3.6.2
hms hms /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.3 NA NA methods, pkgconfig, rlang, vctrs (>= 0.2.1) NA crayon, lubridate, pillar (>= 1.1.0), testthat NA GPL-3 NA NA NA NA no 3.6.1
htmlTable htmlTable /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.13.3 NA NA stringr, knitr (>= 1.6), magrittr (>= 1.5), methods, checkmate, htmlwidgets, htmltools, rstudioapi (>= 0.6) NA testthat, XML, xtable, ztable, Hmisc, reshape, rmarkdown, pander, chron, lubridate, tibble, tidyr (>= 0.7.2), dplyr (>= 0.7.4) NA GPL (>= 3) NA NA NA NA no 3.6.1
htmltools htmltools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.0 NA R (>= 2.14.1) utils, digest, Rcpp, rlang Rcpp markdown, testthat, withr knitr GPL (>= 2) NA NA NA NA yes 3.6.1
htmlwidgets htmlwidgets /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5.1 NA NA grDevices, htmltools (>= 0.3), jsonlite (>= 0.9.16), yaml NA knitr (>= 1.8) shiny (>= 1.1) MIT + file LICENSE NA NA NA NA no 3.6.1
httpcode httpcode /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA NA NA NA testthat NA MIT + file LICENSE NA NA NA NA no 3.6.2
httpuv httpuv /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5.2 NA R (>= 2.15.1) Rcpp (>= 0.11.0), utils, R6, promises, later (>= 0.8.0) Rcpp, BH, later testthat, callr, curl, websocket NA GPL (>= 2) | file LICENSE NA NA NA NA yes 3.6.1
httr httr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.1 NA R (>= 3.2) curl (>= 3.0.0), jsonlite, mime, openssl (>= 0.8), R6 NA covr, httpuv, jpeg, knitr, png, readr, rmarkdown, testthat (>= 0.8.0), xml2 NA MIT + file LICENSE NA NA NA NA no 3.6.1
hunspell hunspell /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0 NA R (>= 3.0.2) Rcpp, digest Rcpp (>= 0.12.12) spelling, testthat, pdftools, janeaustenr, wordcloud2, knitr, stopwords, rmarkdown NA GPL-2 | LGPL-2.1 | MPL-1.1 NA NA NA NA yes 3.6.1
hwriter hwriter /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.2 NA R (>= 2.6.0) NA NA NA NA LGPL-2.1 NA NA NA NA no 3.6.1
igraph igraph /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.5 NA methods graphics, grDevices, magrittr, Matrix, pkgconfig (>= 2.0.0), stats, utils NA ape, digest, graph, igraphdata, rgl, scales, stats4, tcltk, testthat, withr NA GPL (>= 2) NA NA NA NA yes 3.6.2
imager imager /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.42.3 NA R (>= 2.10.0),magrittr Rcpp (>= 0.11.5),methods,stringr,png,jpeg,readbitmap,grDevices,purrr,downloader,igraph Rcpp knitr, rmarkdown,ggplot2,dplyr,scales, testthat,OpenMPController,raster,spatstat, magick,Cairo NA LGPL-3 NA NA NA NA yes 3.6.2
import import /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA NA NA NA knitr NA MIT + file LICENSE NA NA NA NA no 3.6.1
imputeMissings imputeMissings /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0.3 NA NA randomForest,stats NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
inflection inflection /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.5 NA NA parallel, stats, graphics, grDevices NA knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 3.6.2
influenceR influenceR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.0 NA R (>= 3.2.0) igraph (>= 1.0.1), Matrix (>= 1.1-4), methods, utils NA testthat NA GPL-2 NA NA NA NA yes 3.6.1
ini ini /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.1 NA NA NA NA testthat NA GPL-3 NA NA NA NA no 3.6.0
inTrees inTrees /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2 NA NA RRF, arules, gbm, xtable, xgboost, data.table, methods NA NA NA GPL (>= 3) NA NA NA NA no 3.6.0
inum inum /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-1 NA R (>= 3.3.0) stats, libcoin (>= 1.0-0) NA NA NA GPL-2 NA NA NA NA no 3.6.0
ipred ipred /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-9 NA R (>= 2.10) rpart (>= 3.1-8), MASS, survival, nnet, class, prodlim NA mvtnorm, mlbench, TH.data NA GPL (>= 2) NA NA NA NA yes 3.6.0
IRanges IRanges /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.18.3 NA R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.21.9) stats4 S4Vectors XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle NA Artistic-2.0 NA NA NA NA yes 3.6.1
irlba irlba /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3.3 NA Matrix stats, methods Matrix NA NA GPL-3 NA NA NA NA yes 3.6.0
isoband isoband /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.1 NA NA Rcpp, grid, utils Rcpp, testthat covr, ggplot2, knitr, magick, microbenchmark, rmarkdown, sf, testthat NA MIT + file LICENSE NA NA NA NA yes 3.6.2
ISwR ISwR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0-8 NA R (>= 2.6.0) NA NA survival,MASS NA GPL (>= 2) NA NA NA NA no 3.6.2
iterators iterators /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.12 NA R (>= 2.5.0), utils NA NA RUnit, foreach NA Apache License (== 2.0) NA NA NA NA no 3.6.1
itertools itertools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-3 NA R (>= 2.14.0), iterators(>= 1.0.0) parallel NA foreach NA GPL-2 NA NA NA NA no 3.6.0
janitor janitor /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.1 NA R (>= 3.1.2) dplyr (>= 0.7.0), lifecycle, lubridate, magrittr, purrr, rlang, stringi, stringr, snakecase (>= 0.9.2), tidyselect (>= 1.0.0), tidyr (>= 0.7.0) NA knitr, rmarkdown, sf, testthat, tibble, tidygraph NA MIT + file LICENSE NA NA NA NA no 3.6.2
jomo jomo /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.6-10 NA NA stats, lme4, survival, MASS, ordinal NA mitml NA GPL-2 NA NA NA NA yes 3.6.1
jpeg jpeg /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-8.1 NA R (>= 2.9.0) NA NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
jsonlite jsonlite /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.1 NA methods NA NA httr, curl, plyr, testthat, knitr, rmarkdown, R.rsp, sp NA MIT + file LICENSE NA NA NA NA yes 3.6.2
kableExtra kableExtra /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA R (>= 3.1.0) knitr (>= 1.16), magrittr, stringr (>= 1.0), xml2 (>= 1.1.1), rvest, rmarkdown (>= 1.6.0), readr, scales, viridisLite, stats, grDevices, htmltools, rstudioapi, glue, tools, webshot, digest NA testthat, magick, formattable, dplyr NA MIT + file LICENSE NA NA NA NA no 3.6.0
KEGGgraph KEGGgraph /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.44.0 NA R (>= 2.10.0) methods, XML (>= 2.3-0), graph, utils, RCurl NA Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA NA GPL (>= 2) NA NA NA NA no 3.6.1
KEGGREST KEGGREST /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.24.1 NA NA methods, httr, png, Biostrings NA RUnit, BiocGenerics, knitr NA Artistic-2.0 NA NA NA NA no 3.6.1
keras keras /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2.5.0 NA R (>= 3.2) generics (>= 0.0.1), reticulate (>= 1.10), tensorflow (>= 2.0.0), tfruns (>= 1.0), magrittr, zeallot, methods, R6 NA ggplot2, testthat (>= 2.1.0), knitr, rmarkdown, tfdatasets, jpeg NA MIT + file LICENSE NA NA NA NA no 3.6.2
kernlab kernlab /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-29 NA R (>= 2.10) methods, stats, grDevices, graphics NA NA NA GPL-2 NA NA NA NA yes 3.6.2
klaR klaR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6-15 NA R (>= 2.10.0), MASS combinat, questionr, grDevices, stats, utils, graphics NA scatterplot3d (>= 0.3-22), som, mlbench, rpart, e1071 NA GPL-2 | GPL-3 NA NA NA NA no 3.6.2
km.ci km.ci /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5-2 NA R (>= 1.8.0), survival, stats NA NA NA NA GPL (>= 2) NA NA NA NA NA 3.6.0
KMsurv KMsurv /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-5 NA NA NA NA NA NA GPL (>= 3) NA NA NA NA NA 3.6.0
knitcitations knitcitations /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.10 NA R (>= 3.0) RefManageR (>= 0.8.2), digest, httr (>= 0.3), methods, utils NA testthat, knitr (>= 1.6) NA MIT + file LICENSE NA NA NA NA no 3.6.1
knitr knitr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.28 NA R (>= 3.2.3) evaluate (>= 0.10), highr, markdown, stringr (>= 0.6), yaml (>= 2.1.19), methods, xfun, tools NA formatR, testit, digest, rgl (>= 0.95.1201), codetools, rmarkdown, htmlwidgets (>= 0.7), webshot, tikzDevice (>= 0.10), tinytex, reticulate (>= 1.4), JuliaCall (>= 0.11.1), magick, png, jpeg, gifski, xml2 (>= 1.2.0), httr, DBI (>= 0.4-1), showtext, tibble, sass, styler (>= 1.2.0) NA GPL NA NA NA NA no 3.6.2
ks ks /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.11.7 NA R (>= 2.10.0) FNN (>= 1.1), kernlab, KernSmooth (>= 2.22), Matrix, mclust, mgcv, multicool, mvtnorm (>= 1.0-0) NA maps, MASS, misc3d (>= 0.4-0), OceanView, oz, rgl (>= 0.66) NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
labeling labeling /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3 NA NA NA NA NA NA MIT + file LICENSE | Unlimited NA NA NA NA no 3.6.0
labelled labelled /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3.1 NA NA haven (>= 2.1.0), dplyr, stats NA testthat, knitr, rmarkdown, questionr, snakecase memisc GPL-3 NA NA NA NA no 3.6.2
laeken laeken /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.1 NA R (>= 3.2.0) boot, MASS NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
Lahman Lahman /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 7.0-1 NA R (>= 2.10) dplyr NA lattice, ggplot2, googleVis, data.table, vcd, reshape2, tidyr, zipcode, knitr, rmarkdown, car NA GPL NA NA NA NA no 3.6.1
lambda.r lambda.r /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.4 NA R (>= 3.0.0) formatR NA testit NA LGPL-3 NA NA NA NA no 3.6.1
LambertW LambertW /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.4 NA MASS, ggplot2, lamW (>= 1.0.0), stats, graphics, grDevices, RColorBrewer, reshape2, Rcpp Rcpp, lamW boot, Rsolnp, nortest, numDeriv, testthat, moments, NA GPL (>= 2) NA NA NA NA yes 3.6.2
lamW lamW /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.0 NA R (>= 3.0.2) Rcpp, RcppParallel (>= 4.3.20) Rcpp, RcppParallel (>= 4.3.20) testthat NA BSD_2_clause + file LICENSE NA NA NA NA yes 3.6.2
lars lars /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2 NA R (>= 2.10) NA NA NA NA GPL-2 NA NA NA NA yes 3.6.1
later later /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA NA Rcpp (>= 0.12.9), rlang Rcpp, BH knitr, rmarkdown, testthat NA GPL (>= 2) NA NA NA NA yes 3.6.1
latticeExtra latticeExtra /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6-29 NA R (>= 3.6.0), lattice grid, stats, utils, grDevices, png, jpeg, RColorBrewer NA maps, mapproj, deldir, tripack, quantreg, zoo, MASS, mgcv NA GPL (>= 2) NA NA NA NA no 3.6.1
lava lava /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.7 NA R (>= 3.0) grDevices, graphics, methods, numDeriv, stats, survival, SQUAREM, utils NA KernSmooth, Matrix, Rgraphviz, data.table, ellipse, fields, foreach, geepack, gof (>= 0.9), graph, igraph (>= 0.6), lava.tobit (>= 0.4.7), lme4, mets (>= 1.1), nlme, optimx, polycor, quantreg, rgl, testthat (>= 0.11), visNetwork, zoo NA GPL-3 NA NA NA NA no 3.6.2
lava.tobit lava.tobit /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5 NA lava (>= 1.5), mets (>= 1.2.2), mvtnorm, survival NA NA NA NA GPL-3 NA NA NA NA no 3.6.1
lavaan lavaan /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6-5 NA R(>= 3.4) methods, stats4, stats, utils, graphics, MASS, mnormt, pbivnorm, numDeriv NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
lazyeval lazyeval /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.2 NA R (>= 3.1.0) NA NA knitr, rmarkdown (>= 0.2.65), testthat, covr NA GPL-3 NA NA NA NA yes 3.6.0
LDheatmap LDheatmap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.99-7 NA R (>= 2.14.0) grid, genetics, snpStats, Rcpp Rcpp rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, lattice, ggplot2, vcfR NA GPL-3 NA NA NA NA yes 3.6.1
leaps leaps /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.1 NA NA NA biglm NA GPL (>= 2) NA NA NA NA yes 3.6.1
libcoin libcoin /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-5 NA R (>= 3.4.0) stats, mvtnorm mvtnorm coin NA GPL-2 NA NA NA NA yes 3.6.1
LiblineaR LiblineaR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.10-8 NA NA NA NA SparseM NA GPL-2 NA NA NA NA yes 3.6.0
lifecycle lifecycle /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.0 NA R (>= 3.2) glue, rlang (>= 0.4.0) NA covr, crayon, knitr, rmarkdown, testthat (>= 2.1.0) NA GPL-3 NA NA NA NA no 3.6.2
limma limma /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.40.6 NA R (>= 3.6.0) grDevices, graphics, stats, utils, methods NA affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn NA GPL (>=2) NA NA NA NA yes 3.6.1
lintr lintr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.1 NA R (>= 3.2) rex, crayon, codetools, cyclocomp, testthat (>= 2.2.1), digest, rstudioapi (>= 0.2), httr (>= 1.2.1), jsonlite, knitr, stats, utils, xml2 (>= 1.0.0), xmlparsedata (>= 1.0.3) NA rmarkdown, mockery NA MIT + file LICENSE NA NA NA NA no 3.6.2
listenv listenv /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.8.0 NA R (>= 3.1.2) NA NA R.utils, R.rsp, markdown NA LGPL (>= 2.1) NA NA NA NA no 3.6.1
lm.beta lm.beta /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5-1 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
lme4 lme4 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-23 NA R (>= 3.2.0), Matrix (>= 1.2-1), methods, stats graphics, grid, splines, utils, parallel, MASS, lattice, boot, nlme (>= 3.1-123), minqa (>= 1.1.15), nloptr (>= 1.0.4), statmod Rcpp (>= 0.10.5), RcppEigen knitr, rmarkdown, PKPDmodels, MEMSS, testthat (>= 0.8.1), ggplot2, mlmRev, optimx (>= 2013.8.6), gamm4, pbkrtest, HSAUR2, numDeriv, car, dfoptim NA GPL (>= 2) NA NA NA NA yes 3.6.2
lmom lmom /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.8 NA R (>= 3.0.0) stats, graphics NA NA NA Common Public License Version 1.0 NA NA NA NA yes 3.6.1
lmtest lmtest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-37 NA R (>= 3.0.0), stats, zoo graphics NA car, strucchange, sandwich, dynlm, stats4, survival, AER NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
locfit locfit /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5-9.4 NA R (>= 3.5.0) lattice NA interp, gam NA GPL (>= 2) NA NA NA NA yes 3.6.2
logcondens logcondens /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1.5 NA R (>= 2.10) ks, graphics, stats NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
LogicReg LogicReg /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.2 NA R (>= 2.10), survival stats, graphics, utils, grDevices NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
lsr lsr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5 NA NA NA NA NA NA GPL-3 NA NA NA NA no 3.6.0
lubridate lubridate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7.8 NA methods, R (>= 3.2) generics, Rcpp (>= 0.12.13) Rcpp covr, knitr, testthat chron, timeDate, tis, zoo GPL (>= 2) NA NA NA NA yes 3.6.2
magick magick /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3 NA NA Rcpp (>= 0.12.12), magrittr, curl Rcpp av (>= 0.3), spelling, jsonlite, methods, knitr, rmarkdown, rsvg, webp, pdftools, ggplot2, raster, rgdal, gapminder, IRdisplay, tesseract (>= 2.0), gifski NA MIT + file LICENSE NA NA NA NA yes 3.6.2
magrittr magrittr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5 NA NA NA NA testthat, knitr NA MIT + file LICENSE NA NA NA NA no 3.6.0
manipulateWidget manipulateWidget /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.10.1 NA NA shiny (>= 1.0.3), miniUI, htmltools, htmlwidgets, knitr, methods, tools, base64enc, grDevices, codetools, webshot NA dygraphs, leaflet, plotly, xts, rmarkdown, testthat, covr NA GPL (>= 2) | file LICENSE NA NA NA NA no 3.6.2
mapdata mapdata /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3.0 NA R (>= 2.14.0), maps (>= 2.0-7) NA NA NA NA GPL-2 NA NA NA NA yes 3.6.2
mapproj mapproj /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.7 NA R (>= 3.0.0), maps (>= 2.3-0) stats, graphics NA NA NA Lucent Public License NA NA NA NA yes 3.6.2
maps maps /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.3.0 NA R (>= 3.0.0) graphics, utils NA mapproj (>= 1.2-0), mapdata (>= 2.3.0), sp, maptools, rnaturalearth NA GPL-2 NA NA NA NA yes 3.6.1
maptools maptools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-9 NA R (>= 2.10), sp (>= 1.0-11) foreign (>= 0.8), methods, grid, lattice, stats, utils, grDevices NA rgeos (>= 0.1-8), spatstat (>= 1.60), PBSmapping, maps, RColorBrewer, raster, polyclip, spatstat.utils gpclib, RArcInfo GPL (>= 2) NA NA NA NA yes 3.6.1
markdown markdown /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1 NA R (>= 2.11.1) utils, xfun, mime (>= 0.3) NA knitr, RCurl NA GPL-2 NA NA NA NA yes 3.6.1
MASS MASS /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 7.3-51.6 recommended R (>= 3.1.0), grDevices, graphics, stats, utils methods NA lattice, nlme, nnet, survival NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
Matching Matching /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.9-7 NA R (>= 2.6.0), MASS (>= 7.2-1), graphics, grDevices, stats NA NA parallel, rgenoud (>= 2.12), rbounds NA GPL-3 NA NA NA NA yes 3.6.2
MatchIt MatchIt /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0.2 NA R (>= 2.6) MASS, Matching NA cem, nnet, optmatch, rpart, mgcv, WhatIf, R.rsp, testthat, rgenoud NA GPL (>= 2) NA NA NA NA no 3.6.2
matlab matlab /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.2 NA R (>= 2.15) methods NA NA NA Artistic-2.0 NA NA NA NA no 3.6.1
MatrixModels MatrixModels /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-1 NA R (>= 3.0.1) stats, methods, Matrix (>= 1.1-5) NA NA NA GPL (>= 2) NA NA NA NA no 3.6.0
matrixStats matrixStats /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.56.0 NA R (>= 2.12.0) NA NA base64enc, ggplot2, knitr, microbenchmark, R.devices, R.rsp NA Artistic-2.0 NA NA NA NA yes 3.6.2
maxstat maxstat /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7-25 NA R (>= 1.7.0) exactRankTests(>= 0.8-23), mvtnorm(>= 0.5-10), stats, graphics NA TH.data, survival NA GPL (>= 2) NA NA NA NA yes 3.6.0
mboost mboost /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.9-2 NA R (>= 3.2.0), methods, stats, parallel, stabs (>= 0.5-0) Matrix, survival, splines, lattice, nnls, quadprog, utils, graphics, grDevices, partykit (>= 1.2-1) NA TH.data, MASS, fields, BayesX, gbm, mlbench, RColorBrewer, rpart (>= 4.0-3), randomForest, nnet, testthat (>= 0.10.0), kangar00 NA GPL-2 NA NA NA NA yes 3.6.2
mclust mclust /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.4.6 NA R (>= 3.0) stats, utils, graphics, grDevices NA knitr (>= 1.12), rmarkdown (>= 0.9), mix (>= 1.0), geometry (>= 0.3-6), MASS NA GPL (>= 2) NA NA NA NA yes 3.6.2
mda mda /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5 NA R (>= 3.5.0), stats, class NA NA earth, testthat NA GPL-2 NA NA NA NA yes 3.6.2
memisc memisc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.99.22 NA R (>= 3.3.0), lattice, stats, methods, utils, MASS grid, repr, data.table NA splines, knitr, rmarkdown, sandwich AER, car, eha, lme4, ordinal, simex, tibble, haven GPL-2 NA NA NA NA yes 3.6.2
memoise memoise /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA NA digest (>= 0.6.3) NA testthat, aws.s3, httr, covr NA MIT + file LICENSE NA NA NA NA no 3.6.0
mets mets /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.7.1 NA R (>= 3.5), timereg (>= 1.9.4), lava (>= 1.6.6) mvtnorm, numDeriv, compiler, Rcpp, splines, survival (>= 2.43-1), Rcpp, RcppArmadillo, mvtnorm prodlim, testthat (>= 0.11), ucminf, R.rsp (>= 0.40) NA GPL (>= 2) NA NA NA NA yes 3.6.2
mgcv mgcv /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.8-31 recommended R (>= 2.14.0), nlme (>= 3.1-64) methods, stats, graphics, Matrix, splines, utils NA parallel, survival, MASS NA GPL (>= 2) NA NA NA NA yes 3.6.2
mice mice /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.8.0 NA R (>= 2.10.0) broom, dplyr, graphics, lattice, methods, stats, tidyr, utils Rcpp knitr, lme4, MASS, mitml, miceadds, nnet, pan, randomForest, rmarkdown, rpart, survival, testthat NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
microbenchmark microbenchmark /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-7 NA NA graphics, stats NA ggplot2, multcomp, RUnit NA BSD_2_clause + file LICENSE NA NA NA NA yes 3.6.1
mime mime /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9 NA NA tools NA NA NA GPL NA NA NA NA yes 3.6.2
miniUI miniUI /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.1.1 NA NA shiny (>= 0.13), htmltools (>= 0.3), utils NA NA NA GPL-3 NA NA NA NA no 3.6.0
minqa minqa /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.4 NA NA Rcpp (>= 0.9.10) Rcpp NA NA GPL-2 NA NA NA NA yes 3.6.0
OmicSelector OmicSelector /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.0 NA NA dplyr, remotes, devtools, BiocManager, plyr, epiDisplay, rsq, MASS, caret, pROC, ggplot2, DMwR, ROSE, gridExtra, gplots, stringr, data.table, doParallel, Boruta, spFSR, varSelRF, My.stepwise, psych, C50, randomForest, nnet, reticulate, stargazer, ggrepel, classInt, plotly, keras, cutpointr, naniar, visdat, imputeMissings, foreach, deepnet, snow, calibrate, networkD3, VennDiagram, RSNNS, kernlab, car, PairedData, profileR, xgboost, kableExtra NA knitr, rmarkdown, NA License: MIT + file LICENSE NA NA NA NA NA 3.6.2
miRNAtap miRNAtap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.18.0 NA R (>= 3.3.0), AnnotationDbi DBI, RSQLite, stringr, sqldf, plyr, methods NA topGO, org.Hs.eg.db, miRNAtap.db, testthat NA GPL-2 NA NA NA NA no 3.6.1
miRNAtap.db miRNAtap.db /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.99.10 NA miRNAtap AnnotationDbi, DBI, RSQLite, miRNAtap NA NA NA GPL-2 NA NA NA NA no 3.6.1
missForest missForest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4 NA randomForest,foreach,itertools NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.0
mitml mitml /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3-7 NA NA pan, jomo, haven, grDevices, graphics, stats, utils NA mice, miceadds, Amelia, lme4, nlme, geepack, survival, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 3.6.0
mixOmics mixOmics /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 6.8.5 NA R (>= 3.5.0), MASS, lattice, ggplot2 igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, utils NA BiocStyle, knitr, rmarkdown, testthat, rgl NA GPL (>= 2) NA NA NA NA no 3.6.1
mlbench mlbench /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1-1 NA R (>= 2.10) NA NA lattice NA GPL-2 NA NA NA NA NA 3.6.1
MLmetrics MLmetrics /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.1 NA R (>= 2.10) stats, utils, ROCR NA e1071 NA GPL-2 NA NA NA NA no 3.6.1
mlr mlr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.17.1 NA ParamHelpers (>= 1.10), R (>= 3.0.2) backports (>= 1.1.0), BBmisc (>= 1.11), checkmate (>= 1.8.2), data.table (>= 1.12.4), ggplot2, methods, parallelMap (>= 1.3), stats, stringi, survival, utils, XML NA ada, adabag, bartMachine, batchtools, brnn, bst, C50, care, caret (>= 6.0-57), class, clue, cluster, ClusterR, clusterSim (>= 0.44-5), cmaes, cowplot, CoxBoost, crs, Cubist, deepnet, DiceKriging, DiscriMiner, e1071, earth, elasticnet, emoa, evtree, extraTrees, fda.usc, FDboost, FNN, forecast (>= 8.3), fpc, frbs, FSelector, FSelectorRcpp (>= 0.2.1), gbm, GenSA, ggpubr, glmnet, GPfit, h2o (>= 3.6.0.8), Hmisc, hrbrthemes, irace (>= 2.0), kernlab, kknn, klaR, knitr, laGP, LiblineaR, lintr (>= 1.0.0.9001), MASS, mboost, mco, mda, memoise, mlbench, mldr, mlrMBO, mmpf, modeltools, mRMRe, neuralnet, nnet, nodeHarvest (>= 0.7-3), numDeriv, pamr, pander, party, penalized (>= 0.9-47), pls, PMCMR (>= 4.1), praznik (>= 5.0.0), randomForest, randomForestSRC (>= 2.7.0), ranger (>= 0.8.0), rappdirs, refund, rex, rFerns, rgenoud, rknn, rmarkdown, ROCR, rotationForest, rpart, RRF, rrlda, rsm, RSNNS, rucrdtw, RWeka, sda, sf, smoof, sparseLDA, stepPlr, survAUC, svglite, SwarmSVM, testthat, tgp, TH.data, tidyr, tsfeatures, vdiffr, wavelets, xgboost (>= 0.7) NA BSD_2_clause + file LICENSE NA NA NA NA yes 3.6.2
mnormt mnormt /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5-7 NA R (>= 2.2.0) NA NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
mockery mockery /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.2 NA NA testthat NA knitr, rmarkdown (>= 1.0), R6 NA MIT + file LICENSE NA NA NA NA no 3.6.1
mockr mockr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1 NA NA lazyeval NA testthat, covr NA GPL-3 NA NA NA NA no 3.6.1
ModelMetrics ModelMetrics /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.2.2 NA R (>= 3.2.2) Rcpp, data.table Rcpp testthat NA GPL (>= 2) NA NA NA NA yes 3.6.2
modelr modelr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.7 NA R (>= 3.2) broom, dplyr, magrittr, purrr (>= 0.2.2), rlang (>= 0.2.0), tibble, tidyr (>= 0.8.0), tidyselect NA compiler, covr, ggplot2, testthat NA GPL-3 NA NA NA NA no 3.6.2
modeltools modeltools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2-23 NA stats, stats4 methods NA NA NA GPL-2 NA NA NA NA no 3.6.2
moments moments /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.14 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
mRMRe mRMRe /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1.0 NA survival, igraph, methods NA NA NA NA Artistic-2.0 NA NA NA NA yes 3.6.1
mstate mstate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.12 NA survival (>= 3.1) RColorBrewer NA cmprsk NA GPL (>= 2) NA NA NA NA yes 3.6.1
multcomp multcomp /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-13 NA stats, graphics, mvtnorm (>= 1.0-10), survival (>= 2.39-4), TH.data (>= 1.0-2) sandwich (>= 2.3-0), codetools NA lme4 (>= 0.999375-16), nlme, robustbase, coin, MASS, foreign, xtable, lmtest, coxme (>= 2.2-1), SimComp, ISwR, tram (>= 0.2-5) NA GPL-2 NA NA NA NA no 3.6.2
multicool multicool /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-11 NA methods, Rcpp (>= 0.11.2) NA Rcpp NA NA GPL-2 NA NA NA NA yes 3.6.1
munsell munsell /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.0 NA NA colorspace, methods NA ggplot2, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.0
mvtnorm mvtnorm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-0 NA R(>= 3.5.0) stats, methods NA NA NA GPL-2 NA NA NA NA yes 3.6.2
mxnet mxnet /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5.0 NA R (>= 3.4.4) methods, Rcpp (>= 0.12.1), DiagrammeR (>= 0.9.0), visNetwork (>= 1.0.3), data.table, jsonlite, magrittr, stringr Rcpp testthat, mlbench, knitr, rmarkdown, imager, covr NA Apache License (== 2.0) NA NA NA NA NA 3.6.1
My.stepwise My.stepwise /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.0 NA R (>= 3.3.3) car, lmtest, survival, stats NA NA NA GPL (>= 3) NA NA NA NA no 3.6.2
naniar naniar /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.1 NA R (>= 3.1.2) dplyr, ggplot2, purrr, tidyr, tibble (>= 2.0.0), magrittr, stats, visdat, rlang, forcats, viridis, glue, UpSetR NA knitr, rmarkdown, testthat (>= 2.1.0), rpart, rpart.plot, covr, gridExtra, wakefield, vdiffr, here, simputation, imputeTS, gdtools, Hmisc, spelling NA MIT + file LICENSE NA NA NA NA no 3.6.2
networkD3 networkD3 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4 NA R (>= 3.0.0) htmlwidgets (>= 0.3.2), igraph, magrittr NA htmltools (>= 0.2.6), jsonlite, knitr, shiny GPL (>= 3) NA NA NA NA no 3.6.2
neuralnet neuralnet /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.44.2 NA R (>= 2.9.0) grid, MASS, grDevices, stats, utils, Deriv NA testthat NA GPL (>= 2) NA NA NA NA no 3.6.1
nloptr nloptr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.2.1 NA NA NA NA testthat (>= 0.8.1), knitr, rmarkdown, inline (>= 0.3.14) NA LGPL-3 NA NA NA NA yes 3.6.2
NLP NLP /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2-0 NA R (>= 3.2.0) utils NA NA udpipe, spacyr, cleanNLP GPL-3 NA NA NA NA no 3.6.1
nnls nnls /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA NA 3.6.0
NOISeq NOISeq /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.28.0 NA R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) NA NA NA NA Artistic-2.0 NA NA NA NA no 3.6.1
nor1mix nor1mix /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-0 NA NA stats, graphics NA cluster NA GPL (>= 2) NA NA NA NA no 3.6.1
nortest nortest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-4 NA NA stats NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
np np /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.60-10 NA NA boot, cubature, methods, quadprog, quantreg, stats NA MASS NA GPL NA NA NA NA yes 3.6.2
numDeriv numDeriv /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2016.8-1.1 NA R (>= 2.11.1) NA NA NA NA GPL-2 NA NA NA NA no 3.6.0
nycflights13 nycflights13 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA R (>= 3.2) tibble NA dplyr NA CC0 NA NA NA NA no 3.6.1
olsrr olsrr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.3 NA R(>= 3.3) car, data.table, ggplot2, goftest, graphics, gridExtra, nortest, Rcpp, stats, utils Rcpp covr, descriptr, knitr, rmarkdown, testthat, vdiffr, xplorerr NA MIT + file LICENSE NA NA NA NA yes 3.6.2
openintro openintro /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7.1 NA graphics, grDevices, stats, utils, R (>= 2.10) NA NA NA NA GPL-2 | GPL-3 NA NA NA NA no 3.6.0
openssl openssl /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.1 NA NA askpass NA testthat, digest, knitr, rmarkdown, jsonlite, jose, sodium NA MIT + file LICENSE NA NA NA NA yes 3.6.1
openxlsx openxlsx /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.1.5 NA R (>= 3.3.0) grDevices, methods, Rcpp, stats, utils, zip, stringi Rcpp knitr, testthat, roxygen2 NA MIT + file LICENSE NA NA NA NA yes 3.6.2
optimx optimx /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2020-4.2 NA NA numDeriv NA knitr, rmarkdown, setRNG, BB, ucminf, minqa, dfoptim, lbfgsb3c, lbfgs, subplex NA GPL-2 NA NA NA NA no 3.6.2
ordinal ordinal /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2019.12-10 NA R (>= 2.13.0), stats, methods ucminf, MASS, Matrix, numDeriv NA lme4, nnet, xtable, testthat (>= 0.8), tools NA GPL (>= 2) NA NA NA NA yes 3.6.1
ordinalNet ordinalNet /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.7 NA NA stats, graphics NA testthat (>= 1.0.2), MASS (>= 7.3-45), glmnet (>= 2.0-5), penalized (>= 0.9-50), glmnetcr (>= 1.0.3), VGAM (>= 1.0-3), rms (>= 5.1-0) NA MIT + file LICENSE NA NA NA NA yes 3.6.1
org.Hs.eg.db org.Hs.eg.db /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.8.2 NA R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1) methods, AnnotationDbi NA DBI, annotate, RUnit NA Artistic-2.0 NA NA NA NA no 3.6.1
oro.dicom oro.dicom /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.3 NA R (>= 2.14.0) utils, oro.nifti (>= 0.4.0) NA testthat, hwriter NA BSD_3_clause + file LICENSE NA NA NA NA no 3.6.1
oro.nifti oro.nifti /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.10.1 NA R (>= 2.14.0) stats, bitops, splines, graphics, grDevices, methods, utils, abind, RNifti (>= 0.9.0) NA XML, testthat, covr, knitr, rmarkdown dcemriS4, fmri, oro.dicom BSD_3_clause + file LICENSE NA NA NA NA no 3.6.2
pacman pacman /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.1 NA R (>= 3.5.0) remotes, methods, stats, utils NA BiocManager, knitr, lattice, testthat (>= 0.9.0), XML NA GPL-2 NA NA NA NA no 3.6.1
PairedData PairedData /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.1 NA methods,graphics,MASS,gld,mvtnorm,lattice,ggplot2 NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
pamr pamr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.56.1 NA R (>= 2.10), cluster, survival NA NA NA NA GPL-2 NA NA NA NA yes 3.6.1
pan pan /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6 NA NA NA NA mitools, lme4 NA GPL-3 NA no NA NA yes 3.6.0
pander pander /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.3 NA R (>= 2.15.0) grDevices, graphics, methods, utils, stats, digest, tools, Rcpp Rcpp grid, lattice, ggplot2 (>= 0.9.2), sylly, sylly.en, futile.logger, survival, microbenchmark, zoo, nlme, descr, MASS, knitr, rmarkdown, tables, reshape, memisc, Epi, randomForest, tseries, gtable, rms, forecast, data.table NA AGPL-3 | file LICENSE NA NA NA NA yes 3.6.1
parallelMap parallelMap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5.0 NA R (>= 3.0.0) BBmisc (>= 1.8), checkmate (>= 1.8.0), parallel, stats, utils NA BatchJobs (>= 1.8), batchtools (>= 0.9.6), data.table, Rmpi, rpart, snow, testthat NA BSD_2_clause + file LICENSE NA NA NA NA no 3.6.2
ParamHelpers ParamHelpers /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.14 NA NA backports, BBmisc (>= 1.10), checkmate (>= 1.8.2), fastmatch, methods NA akima, covr, eaf, emoa, GGally, ggplot2, grid, gridExtra, irace (>= 2.1), lhs, plyr, reshape2, testthat NA BSD_2_clause + file LICENSE NA NA NA NA yes 3.6.2
parsedate parsedate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.0 NA NA rematch2 NA covr, testthat, withr NA GPL-2 NA NA NA NA yes 3.6.1
party party /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-4 NA R (>= 3.0.0), methods, grid, stats, mvtnorm (>= 1.0-2), modeltools (>= 0.2-21), strucchange survival (>= 2.37-7), coin (>= 1.1-0), zoo, sandwich (>= 1.1-1) mvtnorm TH.data (>= 1.0-3), mlbench, colorspace, MASS, vcd, ipred, varImp NA GPL-2 NA NA NA NA yes 3.6.2
partykit partykit /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2-7 NA R (>= 3.1.0), graphics, grid, libcoin (>= 1.0-0), mvtnorm grDevices, stats, utils, survival, Formula (>= 1.2-1), inum (>= 1.0-0), rpart (>= 4.1-11) NA XML, pmml, rJava, sandwich, strucchange, vcd, AER, mlbench, TH.data (>= 1.0-3), coin (>= 1.1-0), RWeka (>= 0.4-19), datasets, parallel, psychotools (>= 0.3-0), psychotree, party (>= 1.3-0) NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
pastecs pastecs /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.21 NA NA boot, stats, graphics, utils, grDevices NA svUnit, covr NA GPL-2 NA NA NA NA no 3.6.0
PASWR PASWR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1 NA e1071, MASS, lattice NA NA NA NA GPL (>= 2) NA NA NA NA NA 3.6.1
pathview pathview /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.24.0 NA R (>= 2.10), org.Hs.eg.db KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils NA gage, org.Mm.eg.db, RUnit, BiocGenerics NA GPL (>=3.0) NA NA NA NA no 3.6.1
pbapply pbapply /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-2 NA R (>= 3.2.0) parallel NA NA NA GPL-2 NA NA NA NA no 3.6.1
pbivnorm pbivnorm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.0 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
pbkrtest pbkrtest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-8.6 NA R (>= 3.6.0), lme4 (>= 1.1.10) Matrix (>= 1.2.3), parallel, magrittr, MASS, methods NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
pca3d pca3d /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.10.1 NA R (>= 2.10) rgl,ellipse NA knitr NA GPL-2 NA NA NA NA no 3.6.1
pec pec /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2019.11.03 NA R (>= 2.9.0), prodlim (>= 1.4.9) foreach (>= 1.4.2), rms (>= 4.2-0), survival (>= 2.37-7), timereg (>= 1.8.9) NA randomForestSRC, party, cmprsk (>= 2.2-7), rpart, CoxBoost, crrstep, riskRegression (>= 1.0.8), lava (>= 1.4.1), Hmisc (>= 3.14-4) NA GPL (>= 2) NA NA NA NA yes 3.6.1
permute permute /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-5 NA R (>= 2.14.0) stats NA vegan (>= 2.0-0), testthat (>= 0.5), parallel NA GPL-2 NA NA NA NA no 3.6.2
pheatmap pheatmap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.12 NA R (>= 2.0) grid, RColorBrewer, scales, gtable, stats, grDevices, graphics NA NA NA GPL-2 NA NA NA NA no 3.6.1
pillar pillar /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.4 NA NA cli, crayon (>= 1.3.4), fansi, rlang (>= 0.3.0), utf8 (>= 1.1.0), vctrs (>= 0.2.0) NA knitr, lubridate, testthat (>= 2.0.0), withr NA GPL-3 NA NA NA NA no 3.6.2
pingr pingr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.0 NA NA processx, utils NA covr, testthat NA MIT + file LICENSE NA NA NA NA yes 3.6.1
pinp pinp /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0.9 NA NA rmarkdown, knitr NA NA NA GPL-3 NA NA NA NA no 3.6.1
pixmap pixmap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-11 NA methods NA NA NA NA GPL-2 NA NA NA NA NA 3.6.2
pkgbuild pkgbuild /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.8 NA R (>= 3.1) callr (>= 3.2.0), cli, crayon, desc, prettyunits, R6, rprojroot, withr (>= 2.1.2) NA Rcpp, testthat, covr NA GPL-3 NA NA NA NA no 3.6.2
pkgconfig pkgconfig /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.3 NA NA utils NA covr, testthat, disposables (>= 1.0.3) NA MIT + file LICENSE NA NA NA NA no 3.6.1
pkgdown pkgdown /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5.1 NA R (>= 3.1.0) callr (>= 2.0.2), cli, crayon, desc, digest, evaluate, fs (>= 1.3.0), fansi, highlight, httr, magrittr, MASS, memoise, openssl, purrr, processx, rematch2, rlang (>= 0.3.0), rmarkdown (>= 1.1.9007), rstudioapi, tibble, tools, whisker, withr, xml2 (>= 1.3.1), yaml NA covr, htmlwidgets, jsonlite, knitr, leaflet, pkgload (>= 1.0.2), testthat (>= 2.1.0), rticles, rsconnect NA MIT + file LICENSE NA NA NA NA no 3.6.2
pkgload pkgload /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.2 NA NA desc, methods, pkgbuild, rlang, rprojroot, rstudioapi, utils, withr NA bitops, covr, Rcpp, testthat NA GPL-3 NA NA NA NA yes 3.6.0
plogr plogr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.0 NA NA NA NA Rcpp NA MIT + file LICENSE NA NA NA NA no 3.6.0
plotly plotly /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.9.2.1 NA R (>= 3.2.0), ggplot2 (>= 3.0.0) tools, scales, httr, jsonlite (>= 1.6), magrittr, digest, viridisLite, base64enc, htmltools (>= 0.3.6), htmlwidgets (>= 1.3), tidyr, hexbin, RColorBrewer, dplyr, tibble, lazyeval (>= 0.2.0), rlang, crosstalk, purrr, data.table, promises NA MASS, maps, ggthemes, GGally, testthat, knitr, devtools, shiny (>= 1.1.0), shinytest (>= 1.3.0), curl, rmarkdown, vdiffr, Cairo, broom, webshot, listviewer, dendextend, sf, maptools, rgeos, png, IRdisplay, processx, plotlyGeoAssets, forcats NA MIT + file LICENSE NA NA NA NA no 3.6.2
plotmo plotmo /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.5.7 NA R (>= 3.4.0), Formula (>= 1.2-3), plotrix, TeachingDemos NA NA C50 (>= 0.1.0-24), earth (>= 5.1.0), gbm (>= 2.1.1), glmnet (>= 2.0.5), glmnetUtils (>= 1.0.3), MASS (>= 7.3-45), mlr (>= 2.12.1), neuralnet (>= 1.33), partykit (>= 1.2-2), pre (>= 0.5.0), rpart (>= 4.1-10), rpart.plot (>= 2.1.0) NA GPL-3 NA NA NA NA no 3.6.2
plotrix plotrix /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.7-8 NA R (>= 3.5.0) grDevices, graphics, stats, utils NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
pls pls /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.7-2 NA R (>= 2.10) grDevices, graphics, methods, stats NA MASS, parallel, Rmpi, testthat, RUnit NA GPL-2 NA NA NA NA no 3.6.1
plyr plyr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.8.6 NA R (>= 3.1.0) Rcpp (>= 0.11.0) Rcpp abind, covr, doParallel, foreach, iterators, itertools, tcltk, testthat NA MIT + file LICENSE NA NA NA NA yes 3.6.2
pmml pmml /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3.1 NA XML methods, stats, utils, stringr NA ada, amap, arules, caret, clue, data.table, forecast, gbm, glmnet, Matrix, neighbr, nnet, rpart, randomForestSRC (<= 2.5.0), randomForest, rattle, kernlab, e1071, testthat, survival, xgboost, knitr, rmarkdown, covr NA GPL-3 | file LICENSE NA NA NA NA no 3.6.2
png png /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-7 NA R (>= 2.9.0) NA NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
polspline polspline /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.18 NA NA stats, graphics NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.2
polyclip polyclip /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.10-0 NA R (>= 3.0.0) NA NA NA NA BSL NA NA NA NA yes 3.6.1
polycor polycor /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7-10 NA R (>= 3.3.0) stats, mvtnorm, Matrix NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
polynom polynom /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-0 NA NA stats, graphics NA knitr, rmarkdown NA GPL-2 NA NA NA NA no 3.6.0
prabclus prabclus /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3-2 NA R (>= 2.10), MASS, mclust NA NA spdep, spatialreg, bootstrap, maptools, foreign, mvtnorm NA GPL NA NA NA NA no 3.6.1
praise praise /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA NA NA NA testthat NA MIT + file LICENSE NA NA NA NA no 3.6.1
prediction prediction /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.14 NA R (>= 3.5.0) utils, stats, data.table NA datasets, methods, testthat AER, aod, betareg, biglm, brglm, caret, crch, e1071, earth, ff, ffbase, gam (>= 1.15), gee, glmnet, glmx, kernlab, lme4, MASS, mclogit, mda, mlogit, MNP, nlme, nnet, ordinal, plm, pscl, quantreg, rpart, sampleSelection, speedglm, survey (>= 3.31-5), survival, truncreg, VGAM MIT + file LICENSE NA NA NA NA no 3.6.1
preprocessCore preprocessCore /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.46.0 NA NA stats NA NA NA LGPL (>= 2) NA NA NA NA yes 3.6.1
prettyunits prettyunits /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.1 NA NA NA NA codetools, covr, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.2
pROC pROC /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.16.2 NA R (>= 2.14) methods, plyr, Rcpp (>= 0.11.1) Rcpp microbenchmark, tcltk, MASS, logcondens, doParallel, testthat, vdiffr, ggplot2 NA GPL (>= 3) NA NA NA NA yes 3.6.2
processx processx /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.4.2 NA NA ps (>= 1.2.0), R6, utils NA callr (>= 3.2.0), codetools, covr, crayon, curl, debugme, parallel, testthat, withr NA MIT + file LICENSE NA NA NA NA yes 3.6.2
prodlim prodlim /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2019.11.13 NA R (>= 2.9.0) Rcpp (>= 0.11.5), stats, grDevices, graphics, survival, KernSmooth, lava Rcpp NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
profdpm profdpm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.3 NA NA NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
profileModel profileModel /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.0 NA R (>= 2.6.0) NA NA MASS, gnm NA GPL (>= 2) NA NA NA NA no 3.6.1
profileR profileR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3-5 NA ggplot2, RColorBrewer, reshape, lavaan, R (>= 3.0.0) NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
profmem profmem /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.0 NA NA utils NA R.rsp, markdown, microbenchmark NA LGPL (>= 2.1) NA NA NA NA no 3.6.1
profvis profvis /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.6 NA R (>= 3.0) htmlwidgets (>= 0.3.2), stringr NA knitr, ggplot2, rmarkdown, testthat, devtools, shiny, htmltools NA GPL-3 | file LICENSE NA NA NA NA yes 3.6.1
progress progress /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.2 NA NA hms, prettyunits, R6, crayon NA Rcpp, testthat, withr NA MIT + file LICENSE NA NA NA NA no 3.6.0
promises promises /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA NA R6, Rcpp, later, rlang, stats, magrittr later, Rcpp testthat, future, knitr, rmarkdown NA MIT + file LICENSE NA NA NA NA yes 3.6.1
proto proto /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA NA NA NA testthat, covr NA GPL-2 NA NA NA NA no 3.6.1
proxy proxy /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-24 NA R (>= 3.4.0) stats, utils NA cba NA GPL-2 NA NA NA NA yes 3.6.2
ps ps /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.3 NA R (>= 3.1) utils NA callr, covr, curl, pingr, processx (>= 3.1.0), R6, rlang, testthat, tibble NA BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.2
pspearman pspearman /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3-0 NA NA NA NA NA NA GPL-3 NA NA NA NA yes 3.6.2
psych psych /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.9.12.31 NA NA mnormt,parallel,stats,graphics,grDevices,methods,lattice,nlme NA psychTools, GPArotation, lavaan, sem, lme4,Rcsdp, graph, Rgraphviz NA GPL (>= 2) NA NA NA NA no 3.6.2
purrr purrr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.4 NA R (>= 3.2) magrittr (>= 1.5), rlang (>= 0.3.1) NA covr, crayon, dplyr (>= 0.7.8), knitr, rmarkdown, testthat, tibble, tidyselect NA GPL-3 | file LICENSE NA NA NA NA yes 3.6.2
pvclust pvclust /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2-0 NA R (>= 2.10.0) NA NA MASS, parallel NA GPL (>= 2) NA NA NA NA no 3.6.1
qap qap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-1 NA NA NA NA testthat NA GPL-3 NA NA NA NA yes 3.6.1
qtl qtl /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.46-2 NA R (>= 2.14.0) parallel, graphics, stats, utils, grDevices NA testthat NA GPL-3 NA NA NA NA yes 3.6.2
quadprog quadprog /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5-8 NA R (>= 3.1.0) NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
quantmod quantmod /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.17 NA R (>= 3.2.0), xts(>= 0.9-0), zoo, TTR(>= 0.2), methods curl NA DBI,RMySQL,RSQLite,timeSeries,XML,downloader,jsonlite(>= 1.1) NA GPL-3 NA NA NA NA no 3.6.2
quantreg quantreg /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.55 NA R (>= 2.6), stats, SparseM methods, graphics, Matrix, MatrixModels NA tripack, akima, MASS, survival, rgl, logspline, nor1mix, Formula, zoo, R.rsp NA GPL (>= 2) NA NA NA NA yes 3.6.2
questionr questionr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7.0 NA R (>= 2.10) shiny (>= 1.0.5), miniUI, rstudioapi, highr, classInt, htmltools, graphics, stats, utils, labelled (>= 2.0.0) NA memisc, testthat, roxygen2, dplyr, tidyr, janitor, forcats, knitr NA GPL (>= 2) NA NA NA NA no 3.6.0
qvalue qvalue /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.16.0 NA R(>= 2.10) splines, ggplot2, grid, reshape2 NA knitr NA LGPL NA NA NA NA no 3.6.1
qvcalc qvcalc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.2 NA NA NA NA relimp, MASS psychotools, survival GPL-2 | GPL-3 NA NA NA NA no 3.6.2
R.methodsS3 R.methodsS3 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.8.0 NA R (>= 2.13.0) utils NA codetools NA LGPL (>= 2.1) NA NA NA NA no 3.6.2
R.oo R.oo /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.23.0 NA R (>= 2.13.0), R.methodsS3 (>= 1.7.1) methods, utils NA tools NA LGPL (>= 2.1) NA NA NA NA no 3.6.1
R.utils R.utils /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.9.2 NA R (>= 2.14.0), R.oo (>= 1.23.0) methods, utils, tools, R.methodsS3 (>= 1.7.1) NA digest (>= 0.6.10) NA LGPL (>= 2.1) NA NA NA NA no 3.6.2
R6 R6 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.4.1 NA R (>= 3.0) NA NA knitr, microbenchmark, pryr, testthat, ggplot2, scales NA MIT + file LICENSE NA NA NA NA no 3.6.1
randomForest randomForest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.6-14 NA R (>= 3.2.2), stats NA NA RColorBrewer, MASS NA GPL (>= 2) NA NA NA NA yes 3.6.2
ranger ranger /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.12.1 NA R (>= 3.1) Rcpp (>= 0.11.2), Matrix Rcpp, RcppEigen survival, testthat NA GPL-3 NA NA NA NA yes 3.6.1
RANN RANN /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.6.1 NA NA NA NA testthat NA GPL (>= 3) NA NA NA NA yes 3.6.1
rappdirs rappdirs /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.1 NA R (>= 2.14), methods NA NA testthat, roxygen2 NA MIT + file LICENSE NA NA NA NA yes 3.6.1
rARPACK rARPACK /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.11-0 NA NA RSpectra NA Matrix (>= 1.1-0) NA BSD_3_clause + file LICENSE NA NA NA NA no 3.6.1
raster raster /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.1-5 NA sp (>= 1.2-0), R (>= 3.0.0) Rcpp, methods Rcpp rgdal (>= 0.9-1), rgeos (>= 0.3-8), ncdf4, igraph, tcltk, parallel, rasterVis, MASS, sf, testthat NA GPL (>= 3) NA NA NA NA yes 3.6.2
rattle rattle /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.3.0 NA R (>= 3.5.0) stats, utils, ggplot2, grDevices, graphics, magrittr, methods, stringi, stringr, tidyr, dplyr, XML, rpart.plot NA pmml (>= 1.2.13), bitops, colorspace, ada, amap, arules, arulesViz, biclust, cairoDevice, cba, cluster, corrplot, descr, doBy, e1071, ellipse, fBasics, foreign, fpc, gdata, ggdendro, ggraptR, gplots, grid, gridExtra, gtools, gWidgetsRGtk2, hmeasure, Hmisc, kernlab, Matrix, mice, nnet, party, plyr, psych, randomForest, RColorBrewer, readxl, reshape, rggobi, RGtk2, ROCR, RODBC, rpart, scales, SnowballC, survival, timeDate, tm, verification, wskm, xgboost NA GPL (>= 2) NA NA NA NA no 3.6.1
rattle.data rattle.data /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.2 NA R (>= 2.10) NA NA rattle NA GPL-3 NA NA NA NA no 3.6.1
rcmdcheck rcmdcheck /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.3 NA NA callr (>= 3.1.1.9000), cli (>= 1.1.0), crayon, desc (>= 1.2.0), digest, pkgbuild, prettyunits, R6, rprojroot, sessioninfo (>= 1.1.1), utils, withr, xopen NA covr, knitr, mockery, rmarkdown, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.0
RColorBrewer RColorBrewer /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-2 NA R (>= 2.0.0) NA NA NA NA Apache License 2.0 NA NA NA NA no 3.6.0
Rcpp Rcpp /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.4.6 NA NA methods, utils NA tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2) NA GPL (>= 2) NA NA NA NA yes 3.6.2
RcppAnnoy RcppAnnoy /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0.16 NA R (>= 3.1) methods, Rcpp (>= 0.11.3) Rcpp tinytest NA GPL (>= 2) NA NA NA NA yes 3.6.2
RcppArmadillo RcppArmadillo /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9.870.2.0 NA R (>= 3.3.0) Rcpp (>= 0.11.0), stats, utils, methods Rcpp tinytest, Matrix, pkgKitten, reticulate, slam NA GPL (>= 2) NA NA NA NA yes 3.6.2
RcppCNPy RcppCNPy /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.10 NA R (>= 3.1.0) methods, Rcpp Rcpp knitr, rmarkdown, pinp, reticulate NA GPL (>= 2) NA NA NA NA yes 3.6.1
RcppEigen RcppEigen /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.3.7.0 NA R (>= 2.15.1) Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils Rcpp inline, tinytest, pkgKitten, microbenchmark NA GPL (>= 2) | file LICENSE NA NA NA NA yes 3.6.1
RcppHNSW RcppHNSW /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.0 NA NA methods, Rcpp (>= 0.11.3) Rcpp testthat, covr NA GPL-3 NA NA NA NA yes 3.6.1
RcppNumerical RcppNumerical /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-0 NA NA Rcpp Rcpp, RcppEigen knitr, rmarkdown, prettydoc, mvtnorm, RcppEigen NA GPL (>= 2) NA NA NA NA yes 3.6.1
RcppParallel RcppParallel /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.0.1 NA R (>= 3.0.2) NA NA Rcpp, RUnit, knitr, rmarkdown NA GPL-2 NA NA NA NA yes 3.6.2
RcppRoll RcppRoll /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA R (>= 2.15.1) Rcpp Rcpp zoo, testthat NA GPL (>= 2) NA NA NA NA yes 3.6.0
RCurl RCurl /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.98-1.2 NA R (>= 3.4.0), methods bitops NA XML NA BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.2
readbitmap readbitmap /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.5 NA NA bmp, jpeg, png, tiff NA pixmap, testthat NA GPL (>= 2) NA NA NA NA no 3.6.1
readr readr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.1 NA R (>= 3.1) Rcpp (>= 0.12.0.5), tibble, hms (>= 0.4.1), R6, clipr, crayon, methods Rcpp, BH curl, testthat, knitr, rmarkdown, stringi, covr, spelling NA GPL (>= 2) | file LICENSE NA NA NA NA yes 3.6.1
readxl readxl /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.1 NA NA cellranger, Rcpp (>= 0.12.18), tibble (>= 1.3.1), utils progress, Rcpp covr, knitr, rmarkdown, rprojroot (>= 1.1), testthat NA GPL-3 NA NA NA NA yes 3.6.0
rebus rebus /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-3 NA R (>= 3.1.0) rebus.base (>= 0.0-3), rebus.datetimes, rebus.numbers, rebus.unicode (>= 0.0-2) NA testthat NA Unlimited NA NA NA NA no 3.6.1
rebus.base rebus.base /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-3 NA R (>= 3.1.0) stats NA stringi, testthat NA Unlimited NA NA NA NA no 3.6.1
rebus.datetimes rebus.datetimes /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-1 NA R (>= 3.1.0) rebus.base NA stats, testthat NA Unlimited NA NA NA NA no 3.6.1
rebus.numbers rebus.numbers /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-1 NA R (>= 3.1.0) rebus.base, utils NA testthat NA Unlimited NA NA NA NA no 3.6.1
rebus.unicode rebus.unicode /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-2 NA R (>= 3.1.0) rebus.base (>= 0.0-2) NA stringi NA Unlimited NA NA NA NA no 3.6.1
recipes recipes /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.12 NA R (>= 3.1), dplyr generics, glue, gower, ipred, lubridate, magrittr, Matrix, purrr (>= 0.2.3), rlang (>= 0.4.0), stats, tibble, tidyr (>= 0.8.3), tidyselect (>= 0.2.5), timeDate, utils, withr NA covr, ddalpha, dimRed (>= 0.2.2), fastICA, ggplot2, igraph, kernlab, knitr, modeldata, pls, RANN, RcppRoll, rmarkdown, rpart, rsample, RSpectra, testthat (>= 2.1.0), xml2 NA GPL-2 NA NA NA NA no 3.6.2
RefManageR RefManageR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.12 NA R (>= 3.0) xml2, jsonlite, utils, plyr, tools, httr, bibtex (>= 0.4.1), lubridate (>= 1.5.0), stringr, methods NA knitr, testthat, NA GPL-2 | GPL-3 | BSD_3_clause + file LICENSE NA NA NA NA no 3.6.1
reghelper reghelper /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.6 NA R (>= 3.1.0) ggplot2 (>= 1.0.0), stats, nlme, lme4, utils NA testthat (>= 0.8.1) NA GPL-3 NA NA NA NA no 3.6.2
registry registry /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5-1 NA R (>= 2.6.0) utils NA NA NA GPL-2 NA NA NA NA no 3.6.1
regress regress /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-15 NA NA NA NA nlme, MASS NA GPL NA NA NA NA no 3.6.1
rematch rematch /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA NA NA NA covr, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.0
rematch2 rematch2 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1.2 NA NA tibble NA covr, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.2
remote remote /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.1 NA R (>= 2.10), Rcpp (>= 0.10.3), raster, methods grDevices, gridExtra, latticeExtra, mapdata, scales, stats, utils Rcpp maps, lattice, grid, sp NA GPL (>= 3) | file LICENSE NA NA NA NA yes 3.6.2
remotes remotes /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1.1 NA R (>= 3.0.0) methods, stats, tools, utils NA brew, callr, codetools, curl, covr, git2r (>= 0.23.0), knitr, mockery, pkgbuild (>= 1.0.1), pingr, rmarkdown, rprojroot, testthat, withr NA GPL (>= 2) NA NA NA NA no 3.6.2
repr repr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA R (>= 3.0.1) utils, grDevices, htmltools, jsonlite, pillar (>= 1.4.0), base64enc NA methods, highr, Cairo, stringr, testthat, diffobj (>= 0.2.3), leaflet data.table, dplyr, htmlwidgets, vegalite, plotly, geojsonio GPL-3 NA NA NA NA no 3.6.2
reprex reprex /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA R (>= 3.1) callr (>= 2.0.0), clipr (>= 0.4.0), fs, rlang, rmarkdown, utils, whisker, withr NA covr, devtools, fortunes, knitr, miniUI, rprojroot, rstudioapi, shiny, styler (>= 1.0.2), testthat (>= 2.0.0) NA MIT + file LICENSE NA NA NA NA no 3.6.1
repurrrsive repurrrsive /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA R (>= 2.10) tibble, utils NA gapminder, jsonlite, purrr, rprojroot, testthat (>= 2.1.0), wesanderson, xml2 NA CC0 NA NA NA NA no 3.6.1
reshape reshape /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.8.8 NA R (>= 2.6.1) plyr NA NA NA MIT + file LICENSE NA NA NA NA yes 3.6.0
reshape2 reshape2 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.4 NA R (>= 3.1) plyr (>= 1.8.1), Rcpp, stringr Rcpp covr, lattice, testthat (>= 0.8.0) NA MIT + file LICENSE NA NA NA NA yes 3.6.2
reticulate reticulate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.15 NA R (>= 3.0) graphics, jsonlite, Matrix, methods, rappdirs, Rcpp (>= 0.12.7), utils Rcpp callr, knitr, rmarkdown, testthat NA Apache License 2.0 NA NA NA NA yes 3.6.2
rex rex /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.0 NA NA lazyeval NA testthat, knitr, rmarkdown, dplyr, ggplot2, magrittr, Hmisc, stringr, rvest, roxygen2, covr NA MIT + file LICENSE NA NA NA NA no 3.6.2
rgeos rgeos /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5-3 NA R (>= 3.3.0), methods, sp (>= 1.1-0) utils, stats, graphics sp maptools (>= 0.8-5), testthat, XML, maps, rgdal NA GPL (>= 2) NA NA NA NA yes 3.6.2
rgexf rgexf /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.16.0 NA NA XML, igraph, grDevices, utils, servr NA knitr, rmarkdown, testthat, covr NA MIT + file LICENSE NA NA NA NA no 3.6.2
rgl rgl /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.100.54 NA R (>= 3.2.0) graphics, grDevices, stats, utils, htmlwidgets, htmltools, knitr, jsonlite (>= 0.9.20), shiny, magrittr, crosstalk, manipulateWidget (>= 0.9.0) NA MASS, rmarkdown, deldir, orientlib, lattice, misc3d, rstudioapi, magick, plotrix (>= 3.7-3), tripack, interp, alphashape3d, tcltk NA GPL NA NA NA NA yes 3.6.2
Rgraphviz Rgraphviz /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.28.0 NA R (>= 2.6.0), methods, utils, graph, grid stats4, graphics, grDevices NA RUnit, BiocGenerics, XML NA EPL NA NA NA NA yes 3.6.1
rhdf5 rhdf5 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.28.1 NA R (>= 3.5.0), methods Rhdf5lib (>= 1.3.2) Rhdf5lib bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark, dplyr, ggplot2 NA Artistic-2.0 NA NA NA NA yes 3.6.1
Rhdf5lib Rhdf5lib /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.3 NA NA NA NA BiocStyle, knitr, rmarkdown NA Artistic-2.0 NA NA NA NA yes 3.6.1
Rhtslib Rhtslib /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.16.3 NA NA zlibbioc zlibbioc BiocStyle, knitr NA LGPL (>= 2) NA NA NA NA yes 3.6.1
rhub rhub /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.1 NA NA assertthat, callr, cli (>= 1.1.0), crayon, desc, digest, httr, jsonlite, parsedate, pillar, prettyunits, processx, R6, rappdirs, rcmdcheck (>= 1.2.1), rematch, tibble, utils, uuid, whoami, withr NA covr, testthat, knitr, rmarkdown NA MIT + file LICENSE NA NA NA NA no 3.6.1
rio rio /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.16 NA R (>= 2.15.0) tools, stats, utils, foreign, haven (>= 1.1.0), curl (>= 0.6), data.table (>= 1.9.8), readxl (>= 0.1.1), openxlsx, tibble NA datasets, bit64, testthat, knitr, magrittr, clipr, csvy, feather, fst, hexView, jsonlite, readODS (>= 1.6.4), readr, rmatio, xml2 (>= 1.2.0), yaml NA GPL-2 NA NA NA NA no 3.6.0
RISmed RISmed /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1.7 NA R (>= 2.8.0), methods NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.0
rJava rJava /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-12 NA R (>= 2.5.0), methods NA NA NA NA GPL-2 NA NA NA NA yes 3.6.2
rjson rjson /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.20 NA R (>= 3.1.0) NA NA NA NA GPL-2 NA NA NA NA yes 3.6.1
rlang rlang /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.6 NA R (>= 3.2.0) NA NA cli, covr, crayon, glue, magrittr, methods, pillar, rmarkdown, testthat (>= 2.3.0), vctrs (>= 0.2.3) NA GPL-3 NA NA NA NA yes 3.6.2
rmarkdown rmarkdown /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1 NA R (>= 3.0) tools, utils, knitr (>= 1.22), yaml (>= 2.1.19), htmltools (>= 0.3.5), evaluate (>= 0.13), base64enc, jsonlite, mime, tinytex (>= 0.11), xfun, methods, stringr (>= 1.2.0) NA shiny (>= 0.11), tufte, testthat, digest, dygraphs, tibble, fs, pkgdown, callr (>= 2.0.0) NA GPL-3 NA NA NA NA no 3.6.2
rmdformats rmdformats /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.7 NA NA knitr, rmarkdown, bookdown, htmltools NA questionr NA GPL (>= 2) NA NA NA NA no 3.6.2
rmeta rmeta /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0 NA NA grid, stats, graphics NA NA NA GPL-2 NA NA NA NA no 3.6.0
rms rms /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.1-4 NA R (>= 3.5.0), Hmisc (>= 4.3-0), survival (>= 3.1-6), lattice, ggplot2 (>= 2.2), SparseM methods, quantreg, rpart, nlme (>= 3.1-123), polspline, multcomp, htmlTable (>= 1.11.0), htmltools NA boot, tcltk, plotly (>= 4.5.6) NA GPL (>= 2) NA NA NA NA yes 3.6.1
RMySQL RMySQL /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.10.20 NA R (>= 2.8.0), DBI (>= 0.4) methods NA RMariaDB, testthat, curl NA GPL-2 NA NA NA NA yes 3.6.2
rngtools rngtools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5 NA R (>= 3.2.0), methods digest, utils, stats, parallel NA covr, RUnit, testthat NA GPL-3 NA NA NA NA no 3.6.2
RNifti RNifti /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA NA Rcpp (>= 0.11.0) Rcpp testthat (>= 0.11.0), covr, reportr, shades oro.nifti, tractor.base GPL-2 NA NA NA NA yes 3.6.2
robustbase robustbase /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.93-6 NA R (>= 3.1.0) stats, graphics, utils, methods, DEoptimR NA grid, MASS, lattice, boot, cluster, Matrix, robust, fit.models, MPV, xtable, ggplot2, GGally, RColorBrewer, reshape2, sfsmisc, catdata, doParallel, foreach, skewt NA GPL (>= 2) NA NA NA NA yes 3.6.2
ROCR ROCR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-11 NA R (>= 3.6) methods, graphics, grDevices, gplots, stats NA testthat, knitr, rmarkdown NA GPL (>= 2) NA NA NA NA no 3.6.2
RODBC RODBC /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-16 NA R (>= 3.0.0) stats NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
Rook Rook /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-1 NA R (>= 2.13.0) utils, tools, methods, brew NA NA NA GPL-2 NA NA NA NA yes 3.6.1
ROSE ROSE /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.0-3 NA NA NA NA MASS, nnet, rpart, tree NA GPL-2 NA NA NA NA no 3.6.2
rowr rowr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.3 NA R (>= 3.0.1) methods NA NA NA GPL-3 NA NA NA NA no 3.6.0
roxygen2 roxygen2 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 7.1.0 NA R (>= 3.2) brew, commonmark, desc (>= 1.2.0), digest, knitr, methods, pkgload (>= 1.0.2), purrr (>= 0.3.3), R6 (>= 2.1.2), Rcpp (>= 0.11.0), rlang, stringi, stringr (>= 1.0.0), utils, xml2 Rcpp covr, devtools, rmarkdown, testthat (>= 2.1.0), R.methodsS3, R.oo NA GPL (>= 2) NA NA NA NA yes 3.6.2
roxygen2md roxygen2md /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA NA desc, devtools, enc, rex, rlang, tibble, usethis, withr NA rstudioapi, testthat NA GPL-3 NA NA NA NA no 3.6.2
rpart rpart /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 4.1-15 recommended R (>= 2.15.0), graphics, stats, grDevices NA NA survival NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
rpart.plot rpart.plot /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0.8 NA R (>= 3.4.0), rpart (>= 4.1-10) NA NA earth (>= 5.1.0) NA GPL-3 NA NA NA NA no 3.6.1
rpartScore rpartScore /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-1 NA R (>= 2.14.2), rpart NA NA MASS NA GPL (>= 2) NA NA NA NA NA 3.6.0
RPostgreSQL RPostgreSQL /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6-2 NA R (>= 2.9.0), methods, DBI (>= 0.3) NA NA NA NA GPL-2 | file LICENSE NA NA NA NA yes 3.6.1
rprojroot rprojroot /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3-2 NA R (>= 3.0.0) backports NA testthat, mockr, knitr, withr, rmarkdown NA GPL-3 NA NA NA NA no 3.6.0
RRF RRF /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.9.1 NA R (>= 2.5.0), stats NA NA RColorBrewer, MASS NA GPL (>= 2) NA NA NA NA yes 3.6.0
Rsamtools Rsamtools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.3 NA methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6) utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel Rhtslib (>= 1.16.3), S4Vectors, IRanges, XVector, Biostrings GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle NA Artistic-2.0 | file LICENSE NA NA NA NA yes 3.6.1
RSNNS RSNNS /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-12 NA R (>= 2.10.0), methods, Rcpp (>= 0.8.5) NA Rcpp scatterplot3d,NeuralNetTools NA LGPL (>= 2) | file LICENSE NA NA NA NA yes 3.6.2
rsnps rsnps /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA NA plyr, stringr, crul (>= 0.5.2), data.table, XML, xml2, jsonlite NA testthat, knitr NA MIT + file LICENSE NA NA NA NA no 3.6.0
RSpectra RSpectra /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.16-0 NA R (>= 3.0.2) Matrix (>= 1.1-0), Rcpp (>= 0.11.5) Rcpp, RcppEigen (>= 0.3.3.3.0) knitr, rmarkdown, prettydoc NA MPL (>= 2) NA NA NA NA yes 3.6.1
rsq rsq /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0 NA NA methods, stats, MASS, lme4, nlme, numDeriv, Matrix NA NA GPL-2 NA NA NA NA no 3.6.2
RSQLite RSQLite /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2.0 NA R (>= 3.1.0) bit64, blob (>= 1.2.0), DBI (>= 1.1.0), memoise, methods, pkgconfig, Rcpp (>= 0.12.7) BH, plogr (>= 0.2.0), Rcpp DBItest (>= 1.7.0), knitr, rmarkdown, testthat NA LGPL (>= 2.1) NA NA NA NA yes 3.6.1
rstatix rstatix /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.0 NA R (>= 3.3.0) stats, utils, tidyr (>= 1.0.0), purrr, broom, rlang (>= 0.3.1), tibble (>= 2.1.3), dplyr (>= 0.7.1), magrittr, corrplot, tidyselect (>= 1.0.0), car NA knitr, rmarkdown, ggpubr, graphics, emmeans, coin, boot, testthat, spelling NA GPL-2 NA NA NA NA no 3.6.2
rstudioapi rstudioapi /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.11 NA NA NA NA testthat, knitr, rmarkdown, clipr NA MIT + file LICENSE NA NA NA NA no 3.6.2
Rsubread Rsubread /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.34.7 NA NA grDevices, stats, utils NA NA NA GPL-3 NA NA NA NA yes 3.6.1
rsvd rsvd /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.3 NA R (>= 3.2.2) Matrix NA ggplot2, testthat NA GPL (>= 3) NA NA NA NA no 3.6.2
rtracklayer rtracklayer /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.44.4 NA R (>= 3.3), methods, GenomicRanges (>= 1.31.8) XML (>= 1.98-0), BiocGenerics (>= 0.25.1), S4Vectors (>= 0.19.22), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), tools S4Vectors, IRanges, XVector BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit NA Artistic-2.0 + file LICENSE NA NA NA NA yes 3.6.1
RVAideMemoire RVAideMemoire /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-75 NA NA ade4 (>= 1.7-8), boot, car, FactoMineR, graphics, grDevices, lme4 (>= 1.0-4), MASS, mixOmics, nnet, pls, pspearman, stats, utils, vegan (>= 2.4-3) NA dgof, emmeans, ordinal, survival NA GPL-2 NA NA NA NA no 3.6.2
rvcheck rvcheck /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.8 NA R (>= 3.4.0) BiocManager, utils, rlang NA NA NA Artistic-2.0 NA NA NA NA no 3.6.2
rversions rversions /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.1 NA NA curl, utils, xml2 (>= 1.0.0) NA mockery, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.1
rvest rvest /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.5 NA R (>= 3.2), xml2 httr (>= 0.5), magrittr, selectr NA covr, knitr, png, rmarkdown, spelling, stringi (>= 0.3.1), testthat NA GPL-3 NA NA NA NA no 3.6.1
RViennaCL RViennaCL /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7.1.8 NA NA NA NA gpuR NA GPL-3 NA NA NA NA no 3.6.1
RWeka RWeka /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-42 NA R (>= 2.6.0) RWekajars (>= 3.9.3-1), rJava (>= 0.6-3), graphics, stats, utils, grid NA partykit (>= 0.8.0), mlbench, e1071 NA GPL-2 NA NA NA NA no 3.6.2
RWekajars RWekajars /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.9.3-2 NA NA rJava (>= 0.6-3) NA NA NA GPL-2 NA NA NA NA no 3.6.1
S4Vectors S4Vectors /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.22.1 NA R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>= 0.23.3) NA NA IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle NA Artistic-2.0 NA NA NA NA yes 3.6.1
sandwich sandwich /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.5-1 NA R (>= 2.10.0) stats, utils, zoo NA AER, car, geepack, lattice, lmtest, MASS, multiwayvcov, parallel, pcse, plm, pscl, scatterplot3d, stats4, strucchange, survival NA GPL-2 | GPL-3 NA NA NA NA no 3.6.0
scales scales /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.1 NA R (>= 3.2) farver (>= 2.0.3), labeling, lifecycle, munsell (>= 0.5), R6, RColorBrewer, viridisLite NA bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), testthat (>= 2.1.0) NA MIT + file LICENSE NA NA NA NA no 3.6.2
scater scater /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.12.2 NA R (>= 3.6), SingleCellExperiment, ggplot2 BiocGenerics, SummarizedExperiment, Matrix, dplyr, ggbeeswarm, grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel Rcpp, beachmat BiocStyle, biomaRt, beachmat, cowplot, destiny, knitr, mvoutlier, rmarkdown, Rtsne, uwot, testthat, magrittr, pheatmap, Biobase, limma NA GPL-3 NA NA NA NA yes 3.6.0
scatterplot3d scatterplot3d /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3-41 NA R (>= 2.7.0) grDevices, graphics, stats NA NA NA GPL-2 NA NA NA NA no 3.6.1
segmented segmented /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-0 NA NA NA NA NA NA GPL NA NA NA NA no 3.6.1
selectr selectr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-2 NA R (>= 3.0) methods, stringr, R6 NA testthat, XML, xml2 NA BSD_3_clause + file LICENCE NA NA NA NA no 3.6.1
seqinr seqinr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.6-1 NA R (>= 2.10.0) ade4,segmented NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
seriation seriation /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2-8 NA R (>= 2.14.0) TSP, qap, grid, cluster, gclus, dendextend, colorspace, MASS, gplots, registry, methods, stats, grDevices NA biclust, testthat, DendSer, GA NA GPL-3 NA NA NA NA yes 3.6.1
servr servr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.16 NA R (>= 3.0.0) mime (>= 0.2), httpuv (>= 1.4.0), xfun, jsonlite NA tools, later, rstudioapi, knitr (>= 1.9), rmarkdown NA GPL NA NA NA NA no 3.6.2
sessioninfo sessioninfo /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.1 NA NA cli, tools, utils, withr NA callr, covr, mockery, testthat NA GPL-2 NA NA NA NA no 3.6.0
sf sf /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9-3 NA methods, R (>= 3.3.0) classInt (>= 0.4-1), DBI (>= 0.8), graphics, grDevices, grid, magrittr, Rcpp (>= 0.12.18), stats, tools, units (>= 0.6-0), utils Rcpp blob, covr, dplyr (>= 0.8-3), ggplot2, knitr, lwgeom (>= 0.2-1), maps, mapview, microbenchmark, odbc, pillar, pool, raster, rgdal, rgeos, rlang, rmarkdown, RPostgres (>= 1.1.0), RPostgreSQL, RSQLite, sp (>= 1.2-4), spatstat, spatstat.utils, stars (>= 0.2-0), testthat, tibble (>= 1.4.1), tidyr (>= 1.0-0), tmap (>= 2.0), vctrs NA GPL-2 | MIT + file LICENSE NA NA NA NA yes 3.6.2
shape shape /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.4 NA R (>= 2.01) stats, graphics, grDevices NA NA NA GPL (>= 3) NA NA NA NA no 3.6.1
shiny shiny /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.0.2 NA R (>= 3.0.2), methods utils, grDevices, httpuv (>= 1.5.2), mime (>= 0.3), jsonlite (>= 0.9.16), xtable, digest, htmltools (>= 0.4.0), R6 (>= 2.0), sourcetools, later (>= 1.0.0), promises (>= 1.1.0), tools, crayon, rlang (>= 0.4.0), fastmap (>= 1.0.0) NA datasets, Cairo (>= 1.5-5), testthat (>= 2.1.1), knitr (>= 1.6), markdown, rmarkdown, ggplot2, reactlog (>= 1.0.0), magrittr, yaml NA GPL-3 | file LICENSE NA NA NA NA no 3.6.2
shinythemes shinythemes /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.2 NA R (>= 3.0.0) shiny (>= 0.11) NA NA NA GPL-3 | file LICENSE NA NA NA NA no 3.6.1
ShortRead ShortRead /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.42.0 NA BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra, S4Vectors, IRanges, XVector, Biostrings BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi NA Artistic-2.0 NA NA NA NA yes 3.6.1
SingleCellExperiment SingleCellExperiment /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.0 NA SummarizedExperiment S4Vectors, methods, BiocGenerics, utils, stats NA testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne, Matrix NA GPL-3 NA NA NA NA no 3.6.0
slam slam /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-47 NA R (>= 3.4.0) stats NA NA Matrix, SparseM, spam GPL-2 NA NA NA NA yes 3.6.1
snakecase snakecase /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.11.0 NA R (>= 3.2) stringr, stringi NA testthat, covr, tibble, purrrlyr, knitr, rmarkdown, magrittr NA GPL-3 NA NA NA NA no 3.6.2
snow snow /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-3 NA R (>= 2.13.1), utils NA NA Rmpi,rlecuyer,nws NA GPL NA NA NA NA no 3.6.2
SnowballC SnowballC /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7.0 NA NA NA NA NA NA BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.2
snpStats snpStats /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.34.0 NA R(>= 2.10.0), survival, Matrix, methods graphics, grDevices, stats, utils, BiocGenerics, zlibbioc NA hexbin NA GPL-3 NA NA NA NA yes 3.6.1
sourcetools sourcetools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.7 NA R (>= 3.0.2) NA NA testthat NA MIT + file LICENSE NA NA NA NA yes 3.6.0
sp sp /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-1 NA R (>= 3.0.0), methods utils, stats, graphics, grDevices, lattice, grid NA RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat, maptools, deldir NA GPL (>= 2) NA NA NA NA yes 3.6.2
spam spam /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.5-1 NA R (>= 3.1), dotCall64, grid, methods NA NA spam64, fields, SparseM, Matrix, testthat, R.rsp, truncdist, knitr, rmarkdown NA LGPL-2 | BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.1
SparseM SparseM /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.78 NA R (>= 2.15), methods graphics, stats, utils NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
spelling spelling /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.1 NA NA commonmark, xml2, hunspell (>= 3.0), knitr NA pdftools NA MIT + file LICENSE NA NA NA NA no 3.6.1
spFSR spFSR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA mlr (>= 2.11), parallelMap (>= 1.3), parallel (>= 3.4.2), tictoc (>= 1.0) ggplot2 (>= 2.2.1), class (>= 7.3), mlbench (>= 2.1) NA caret (>= 6.0), MASS (>= 7.3), knitr, rmarkdown NA GPL-3 NA NA NA NA no 3.6.2
SpidermiR SpidermiR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.14.0 NA R (>= 3.0.0) networkD3, httr, igraph, utils, stats, miRNAtap, miRNAtap.db, AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots, grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks, gdata NA BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 NA GPL (>= 3) NA NA NA NA no 3.6.1
spls spls /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2-3 NA R (>= 2.14) MASS, nnet, parallel, pls NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
sqldf sqldf /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4-11 NA R (>= 3.1.0), gsubfn (>= 0.6), proto, RSQLite DBI, chron NA RH2, RMySQL, RPostgreSQL, svUnit, tcltk, MASS NA GPL-2 NA NA NA NA no 3.6.1
SQUAREM SQUAREM /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2020.2 NA R (>= 3.0) NA NA setRNG NA GPL (>= 2) NA NA NA NA no 3.6.2
stabledist stabledist /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7-1 NA R (>= 3.1.0) stats NA Matrix, fBasics, FMStable, RUnit, Rmpfr, sfsmisc NA GPL (>= 2) NA NA NA NA no 3.6.1
stabs stabs /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6-3 NA R (>= 2.14.0), methods, stats, parallel graphics, grDevices, utils NA glmnet, lars, mboost (> 2.3-0), gamboostLSS (>= 1.2-0), QUIC, TH.data, hdi, testthat, knitr, rmarkdown, igraph, huge NA GPL-2 NA NA NA NA no 3.6.0
stargazer stargazer /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 5.2.2 NA NA stats, utils NA NA AER, betareg, brglm, censReg, dynlm, eha, erer, ergm, fGarch, gee, glmx, gmm, lfe, lme4, lmtest, MASS, mclogit, mgcv, mlogit, mnlogit, nlme, nnet, ordinal, plm, pscl, quantreg, rms, relevent, robustbase, sampleSelection, spdep, survey, survival, Zelig GPL (>= 2) NA NA NA NA no 3.6.2
statmod statmod /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.34 NA R (>= 3.0.0) stats, graphics NA MASS, tweedie NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
stepPlr stepPlr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.93 NA R (>= 2.0) NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.1
stringdist stringdist /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.9.5.5 NA R (>= 2.15.3) parallel NA tinytest NA GPL-3 NA NA NA NA yes 3.6.1
stringi stringi /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.6 NA R (>= 2.14) tools, utils, stats NA NA NA file LICENSE yes NA NA NA yes 3.6.2
stringr stringr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.0 NA R (>= 3.1) glue (>= 1.2.0), magrittr, stringi (>= 1.1.7) NA covr, htmltools, htmlwidgets, knitr, rmarkdown, testthat NA GPL-2 | file LICENSE NA NA NA NA no 3.6.2
strucchange strucchange /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.5-2 NA R (>= 2.10.0), zoo, sandwich graphics, stats, utils NA stats4, car, dynlm, e1071, foreach, lmtest, mvtnorm, tseries NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
subselect subselect /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.15.2 NA R (>= 3.5.0) MASS, ISwR, corpcor NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.2
SummarizedExperiment SummarizedExperiment /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.14.1 NA R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase, DelayedArray (>= 0.3.20) utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.17.25), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.13.1) NA annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit, testthat NA Artistic-2.0 NA NA NA NA no 3.6.1
superpc superpc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.09 NA survival NA NA NA NA GPL-2 NA NA NA NA NA 3.6.1
SuppDists SuppDists /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-9.5 NA R (>= 3.3.0) NA NA RcppZiggurat NA GPL (>= 2) NA NA NA NA yes 3.6.1
survAUC survAUC /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-5 NA R (>= 2.6.0), survival NA NA rms NA GPL-2 NA NA NA NA NA 3.6.0
survcomp survcomp /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.34.0 NA survival, prodlim, R (>= 3.4) ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics NA Hmisc, CPE, clinfun, xtable, Biobase, BiocManager NA Artistic-2.0 NA NA NA NA yes 3.6.0
survival survival /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.1-12 recommended R (>= 3.4.0) graphics, Matrix, methods, splines, stats, utils NA NA NA LGPL (>= 2) NA NA NA NA yes 3.6.2
survivalROC survivalROC /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.3 NA R (>= 1.6.1) NA NA NA NA GPL (>= 2) NA NA NA NA NA 3.6.0
survminer survminer /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.6 NA ggplot2, ggpubr(>= 0.1.6) grid, gridExtra (>= 2.0), magrittr, maxstat, methods, scales, survival, stats, broom, dplyr, tidyr, survMisc, purrr, tibble NA knitr, flexsurv, cmprsk NA GPL-2 NA NA NA NA no 3.6.1
survMisc survMisc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.5 NA survival graphics, grDevices, stats, utils, knitr, KMsurv, ggplot2, data.table, zoo, grid, gridExtra, km.ci, xtable NA NA NA GPL-2 NA NA NA NA no 3.6.0
Sushi Sushi /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.22.0 NA R (>= 2.10), zoo,biomaRt graphics, grDevices NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
sva sva /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.32.1 NA R (>= 3.2), mgcv, genefilter, BiocParallel matrixStats, stats, graphics, utils, limma, NA pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat NA Artistic-2.0 NA NA NA NA yes 3.6.1
svglite svglite /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.3 NA R (>= 3.0.0) Rcpp, gdtools (>= 0.1.6) Rcpp, gdtools, BH htmltools, testthat, xml2 (>= 1.0.0), covr, fontquiver (>= 0.2.0), knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 3.6.2
swirl swirl /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.4.5 NA R (>= 3.1.0) stringr, testthat (>= 1.0.2), httr (>= 1.1.0), yaml, RCurl, digest, tools, methods NA stringi NA MIT + file LICENSE NA NA NA NA no 3.6.1
synbreed synbreed /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.12-9 NA R (>= 2.14) abind, BGLR, doBy, doParallel, foreach, igraph, lattice, qtl, regress (>= 1.3-8), MASS, methods, LDheatmap NA synbreedData (>= 1.5) NA GPL-3 NA NA NA NA no 3.6.1
sys sys /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.3 NA NA NA NA unix (>= 1.4), spelling, testthat NA MIT + file LICENSE NA NA NA NA yes 3.6.1
systemfonts systemfonts /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2.1 NA NA NA NA testthat (>= 2.1.0), covr, knitr, rmarkdown, tools NA MIT + file LICENSE NA NA NA NA yes 3.6.2
TCGAbiolinks TCGAbiolinks /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.12.6 NA R (>= 3.5) downloader (>= 0.4), survminer, grDevices, dplyr, gridExtra, graphics, tibble, grid, GenomicRanges, XML (>= 3.98.0), data.table, EDASeq (>= 2.0.0), edgeR (>= 3.0.0), jsonlite (>= 1.0.0), plyr, knitr, methods, biomaRt, ggplot2, ggthemes, survival, stringr (>= 1.0.0), IRanges, scales, rvest (>= 0.3.0), stats, utils, selectr, S4Vectors, ComplexHeatmap (>= 1.10.2), R.utils, SummarizedExperiment (>= 1.4.0), genefilter, ConsensusClusterPlus, readr, RColorBrewer, doParallel, GenomeInfoDb, GenomicFeatures, parallel, tools, tidyr, sva, limma, purrr, xml2, httr (>= 1.2.1), matlab, circlize, ggrepel (>= 0.6.3) NA jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, igraph, supraHex NA GPL (>= 3) NA NA NA NA no 3.6.1
TeachingDemos TeachingDemos /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.12 NA R (>= 2.10) NA NA tkrplot, lattice, MASS, rgl, tcltk, tcltk2, png, ggplot2, logspline, maptools, R2wd, manipulate NA Artistic-2.0 NA NA NA NA no 3.6.2
tensorflow tensorflow /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2.0 NA R (>= 3.1) config, jsonlite (>= 1.2), processx, reticulate (>= 1.10), tfruns (>= 1.0), utils, yaml, rstudioapi (>= 0.7) NA testthat (>= 2.1.0), keras, tfestimators, callr NA Apache License 2.0 NA NA NA NA no 3.6.2
testthat testthat /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.3.2 NA R (>= 3.1) cli, crayon (>= 1.3.4), digest, ellipsis, evaluate, magrittr, methods, pkgload, praise, R6 (>= 2.2.0), rlang (>= 0.4.1), withr (>= 2.0.0) NA covr, curl (>= 0.9.5), devtools, knitr, rmarkdown, usethis, vctrs (>= 0.1.0), xml2 NA MIT + file LICENSE NA NA NA NA yes 3.6.2
tfruns tfruns /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4 NA R (>= 3.1) utils, jsonlite (>= 1.2), base64enc, yaml, config, magrittr, whisker, tidyselect, rlang, rstudioapi (>= 0.7), reticulate NA testthat, knitr NA Apache License 2.0 NA NA NA NA no 3.6.1
TH.data TH.data /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-10 NA R (>= 2.10.0), survival, MASS NA NA dplyr, gdata, plyr NA GPL-3 NA NA NA NA no 3.6.0
tibble tibble /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.0.1 NA R (>= 3.1.0) cli, crayon (>= 1.3.4), ellipsis (>= 0.2.0), fansi (>= 0.4.0), lifecycle (>= 0.2.0), magrittr, methods, pillar (>= 1.4.3), pkgconfig, rlang (>= 0.4.3), utils, vctrs (>= 0.2.4) NA bench, bit64, blob, covr, dplyr, evaluate, hms, htmltools, import, knitr, mockr, nycflights13, purrr, rmarkdown, testthat (>= 2.1.0), tidyr, withr NA MIT + file LICENSE NA NA NA NA yes 3.6.2
tictoc tictoc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0 NA R (>= 3.0.3), methods NA NA NA NA Apache License (== 2.0) | file LICENSE NA NA NA NA no 3.6.1
tidygraph tidygraph /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.2.0 NA NA tibble, dplyr (>= 0.8.5), igraph, magrittr, utils, rlang, R6, Rcpp, tools, stats, tidyr, pillar Rcpp network, data.tree, ape, graph, methods, testthat, covr, seriation, netrankr, influenceR, NetSwan NA MIT + file LICENSE NA NA NA NA yes 3.6.2
tidyr tidyr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.3 NA R (>= 3.1) dplyr (>= 0.8.2), ellipsis (>= 0.1.0), glue, magrittr, purrr, Rcpp, rlang, stringi, tibble (>= 2.1.1), tidyselect (>= 0.2.5), utils, vctrs (>= 0.2.0), lifecycle Rcpp covr, jsonlite, knitr, repurrrsive (>= 1.0.0), rmarkdown, readr, testthat (>= 2.1.0) NA MIT + file LICENSE NA NA NA NA yes 3.6.2
tidyselect tidyselect /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 NA R (>= 3.2) ellipsis, glue (>= 1.3.0), purrr (>= 0.3.2), rlang (>= 0.4.6), vctrs (>= 0.2.2) NA covr, crayon, dplyr, knitr, magrittr, rmarkdown, testthat (>= 2.3.0), tibble (>= 2.1.3), withr NA GPL-3 NA NA NA NA yes 3.6.2
tidyverse tidyverse /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.0 NA R (>= 3.2) broom (>= 0.5.2), cli (>= 1.1.0), crayon (>= 1.3.4), dbplyr (>= 1.4.2), dplyr (>= 0.8.3), forcats (>= 0.4.0), ggplot2 (>= 3.2.1), haven (>= 2.2.0), hms (>= 0.5.2), httr (>= 1.4.1), jsonlite (>= 1.6), lubridate (>= 1.7.4), magrittr (>= 1.5), modelr (>= 0.1.5), pillar (>= 1.4.2), purrr (>= 0.3.3), readr (>= 1.3.1), readxl (>= 1.3.1), reprex (>= 0.3.0), rlang (>= 0.4.1), rstudioapi (>= 0.10), rvest (>= 0.3.5), stringr (>= 1.4.0), tibble (>= 2.1.3), tidyr (>= 1.0.0), xml2 (>= 1.2.2) NA covr, feather, glue, knitr, rmarkdown, testthat NA GPL-3 | file LICENSE NA NA NA NA no 3.6.2
tiff tiff /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-5 NA R (>= 2.9.0) NA NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
timeDate timeDate /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3043.102 NA R (>= 2.15.1), graphics, utils, stats, methods NA NA date, RUnit NA GPL (>= 2) NA NA NA NA no 3.6.0
timereg timereg /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.9.4 NA R (>= 2.15), survival lava, numDeriv, stats, graphics, grDevices, utils, methods NA mets, NA GPL (>= 2) NA NA NA NA yes 3.6.1
timeSeries timeSeries /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3062.100 NA R (>= 2.10), graphics, grDevices, stats, methods, utils, timeDate (>= 2150.95) NA NA RUnit, robustbase, xts, PerformanceAnalytics, fTrading NA GPL (>= 2) NA NA NA NA no 3.6.2
tinytex tinytex /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.22 NA NA xfun (>= 0.5) NA testit, rstudioapi NA MIT + file LICENSE NA NA NA NA no 3.6.2
tm tm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7-7 NA R (>= 3.2.0), NLP (>= 0.2-0) Rcpp, parallel, slam (>= 0.1-37), stats, tools, utils, graphics, xml2 BH, Rcpp antiword, filehash, methods, pdftools, Rcampdf, Rgraphviz, Rpoppler, SnowballC, testthat, tm.lexicon.GeneralInquirer NA GPL-3 NA NA NA NA yes 3.6.1
triebeard triebeard /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA NA Rcpp Rcpp knitr, rmarkdown, testthat NA MIT + file LICENSE NA NA NA NA yes 3.6.0
truncnorm truncnorm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0-8 NA R (>= 3.4.0) NA NA testthat NA GPL (>= 2) NA NA NA NA yes 3.6.1
TSP TSP /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-10 NA R (>= 3.5.0) graphics, foreach, utils, stats, grDevices NA sp, maps, maptools, testthat NA GPL-3 NA NA NA NA yes 3.6.2
TTR TTR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.23-6 NA NA xts (>= 0.10-0), zoo, curl xts RUnit quantmod GPL (>= 2) NA NA NA NA yes 3.6.1
tweeDEseq tweeDEseq /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.30.0 NA R (>= 2.12.0) MASS, limma, edgeR, parallel, cqn NA tweeDEseqCountData, xtable NA GPL (>= 2) NA NA NA NA yes 3.6.1
tweenr tweenr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA R (>= 3.2.0) Rcpp (>= 0.12.3), grDevices, farver, magrittr, rlang Rcpp testthat, covr NA MIT + file LICENSE NA NA NA NA yes 3.6.1
ucminf ucminf /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1-4 NA NA NA NA numDeriv NA GPL (>= 2) NA NA NA NA yes 3.6.0
units units /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6-6 NA R (>= 3.0.2) Rcpp Rcpp (>= 0.12.10) udunits2, NISTunits, measurements, xml2, tibble, pillar (>= 1.3.0), knitr, testthat, ggforce, rmarkdown, magrittr NA GPL-2 NA NA NA NA yes 3.6.2
UpSetR UpSetR /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.0 NA R (>= 3.0) ggplot2, gridExtra, plyr, utils, stats, methods, grDevices, scales NA knitr NA MIT + file LICENSE NA NA NA NA no 3.6.1
urltools urltools /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.7.3 NA R (>= 2.10) Rcpp, methods, triebeard Rcpp testthat, knitr NA MIT + file LICENSE NA NA NA NA yes 3.6.0
usethis usethis /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.1 NA R (>= 3.2) clipr (>= 0.3.0), cli, crayon, curl (>= 2.7), desc, fs (>= 1.3.0), gh (>= 1.1.0), git2r (>= 0.23), glue (>= 1.3.0), purrr, rematch2, rlang (>= 0.4.3), rprojroot (>= 1.2), rstudioapi, stats, utils, whisker, withr, yaml NA covr, knitr, magick, pkgdown (>= 1.4.0), rmarkdown, roxygen2, spelling (>= 1.2), styler (>= 1.2.0), testthat (>= 2.1.0) NA GPL-3 NA NA NA NA no 3.6.2
utf8 utf8 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.1.4 NA R (>= 2.10) NA NA knitr, rmarkdown, testthat NA Apache License (== 2.0) | file LICENSE NA NA NA NA yes 3.6.0
uuid uuid /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1-4 NA R (>= 2.9.0) NA NA NA NA MIT + file LICENSE NA NA NA NA yes 3.6.2
varSelRF varSelRF /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.7-8 NA R (>= 2.0.0), randomForest, parallel NA NA NA NA GPL (>= 2) NA NA NA NA no 3.6.2
vcd vcd /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4-7 NA R (>= 2.4.0), grid stats, utils, MASS, grDevices, colorspace, lmtest NA KernSmooth, mvtnorm, kernlab, HSAUR, coin NA GPL-2 NA NA NA NA no 3.6.2
vctrs vctrs /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA R (>= 3.2) ellipsis (>= 0.2.0), digest, glue, rlang (>= 0.4.5) NA bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr, pillar (>= 1.4.4), pkgdown, rmarkdown, testthat (>= 2.3.0), tibble, withr, xml2, zeallot NA GPL-3 NA NA NA NA yes 3.6.2
vdiffr vdiffr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.1 NA R (>= 3.2.0) devtools, diffobj, fontquiver (>= 0.2.0), freetypeharfbuzz (>= 0.2.5), gdtools, glue, grDevices, htmlwidgets (>= 0.6), htmltools, purrr (>= 0.2.0), rlang, R6, Rcpp, shiny, testthat (>= 1.0.0), usethis (>= 1.4.0), xml2 (>= 1.0.0) freetypeharfbuzz, gdtools, Rcpp, BH crayon, ggplot2 (>= 3.2.0), roxygen2, rstudioapi, withr, yaml NA GPL-3 | file LICENSE NA NA NA NA yes 3.6.1
vegan vegan /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.5-6 NA permute (>= 0.9-0), lattice, R (>= 3.4.0) MASS, cluster, mgcv NA parallel, tcltk, knitr NA GPL-2 NA NA NA NA yes 3.6.2
VennDiagram VennDiagram /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.6.20 NA R (>= 2.14.1), grid (>= 2.14.1), futile.logger NA NA testthat NA GPL-2 NA NA NA NA no 3.6.2
verification verification /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.42 NA R (>= 2.10), methods, fields, boot, CircStats, MASS, dtw graphics, stats NA NA NA GPL (>= 2) NA NA NA NA no 3.6.1
VIM VIM /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 6.0.0 NA R (>= 3.5.0),colorspace,grid car, grDevices, magrittr, robustbase, stats, sp, vcd,MASS,nnet,e1071,methods,Rcpp,utils,graphics,laeken,ranger, data.table(>= 1.9.4) Rcpp dplyr, testthat (>= 2.1.0), knitr, rmarkdown NA GPL (>= 2) NA NA NA NA yes 3.6.2
vipor vipor /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4.5 NA R (>= 3.0.0) stats, graphics NA testthat, beeswarm, lattice, ggplot2, beanplot, vioplot, ggbeeswarm, NA GPL (>= 2) NA NA NA NA no 3.6.0
viridis viridis /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.1 NA R (>= 2.10), viridisLite (>= 0.3.0) stats, ggplot2 (>= 1.0.1), gridExtra NA hexbin (>= 1.27.0), scales, MASS, knitr, dichromat, colorspace, rasterVis, httr, mapproj, vdiffr, svglite (>= 1.2.0), testthat, covr, rmarkdown, rgdal NA MIT + file LICENSE NA NA NA NA no 3.6.0
viridisLite viridisLite /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.3.0 NA R (>= 2.10) NA NA hexbin (>= 1.27.0), ggplot2 (>= 1.0.1), testthat, covr NA MIT + file LICENSE NA NA NA NA no 3.6.0
visdat visdat /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.3 NA R (>= 3.2.2) ggplot2, tidyr, dplyr, purrr, readr, magrittr, stats, tibble, glue NA testthat, plotly (>= 4.5.6), knitr, rmarkdown, vdiffr, gdtools, spelling NA MIT + file LICENSE NA NA NA NA no 3.6.2
visNetwork visNetwork /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.9 NA R (>= 3.0) htmlwidgets, htmltools, jsonlite, magrittr, utils, methods, grDevices, stats NA knitr, rmarkdown, webshot, igraph, rpart, shiny, shinyWidgets, colourpicker, sparkline, ggraph, tidygraph, flashClust NA MIT + file LICENSE NA NA NA NA no 3.6.1
vsn vsn /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.52.0 NA R (>= 3.4.0), Biobase methods, affy, limma, lattice, ggplot2 NA affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat NA Artistic-2.0 NA NA NA NA yes 3.6.1
webshot webshot /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.5.2 NA R (>= 3.0) magrittr, jsonlite, callr NA httpuv, knitr, rmarkdown, shiny NA GPL-2 NA NA NA NA no 3.6.1
weights weights /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA Hmisc, gdata, mice NA NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.2
whisker whisker /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.4 NA NA NA NA markdown NA GPL-3 NA NA NA NA no 3.6.1
whoami whoami /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.0 NA NA httr, jsonlite, utils NA covr, mockery, testthat, withr NA MIT + file LICENSE NA NA NA NA no 3.6.1
withr withr /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2.0 NA R (>= 3.2.0) graphics, grDevices, stats NA covr, DBI, knitr, lattice, methods, rmarkdown, RSQLite, testthat (>= 2.1.0) NA GPL (>= 2) NA NA NA NA no 3.6.2
wskm wskm /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.4.40 NA R (>= 2.10), grDevices, stats, lattice, latticeExtra, fpc NA NA NA NA GPL (>= 3) NA NA NA NA yes 3.6.2
xfun xfun /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.13 NA NA stats, tools NA testit, parallel, rstudioapi, tinytex, mime, markdown, knitr, htmltools, base64enc, remotes, rmarkdown NA MIT + file LICENSE NA NA NA NA no 3.6.2
xgboost xgboost /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0.2 NA R (>= 3.3.0) Matrix (>= 1.1-0), methods, data.table (>= 1.9.6), magrittr (>= 1.5), stringi (>= 0.5.2) NA knitr, rmarkdown, ggplot2 (>= 1.0.1), DiagrammeR (>= 0.9.0), Ckmeans.1d.dp (>= 3.3.1), vcd (>= 1.3), testthat, lintr, igraph (>= 1.0.1), jsonlite, float NA Apache License (== 2.0) | file LICENSE NA NA NA NA yes 3.6.2
XLConnect XLConnect /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.1 NA R (>= 2.10.0) methods, rJava NA RUnit, lattice, ggplot2 (>= 0.9.3), zoo NA GPL-3 NA NA NA NA no 3.6.2
XLConnectJars XLConnectJars /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.2-15 NA NA rJava NA NA NA GPL-3 NA NA NA NA no 3.6.1
xlsx xlsx /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.3 NA NA rJava, xlsxjars, grDevices, utils NA rprojroot, testthat, covr, tibble, knitr, rmarkdown, RefManageR NA GPL-3 NA NA NA NA no 3.6.2
xlsxjars xlsxjars /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.6.1 NA rJava NA NA NA NA GPL-3 NA NA NA NA no 3.6.0
XML XML /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 3.99-0.3 NA R (>= 2.13.0), methods, utils NA NA bitops, RCurl NA BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.2
xml2 xml2 /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.3.2 NA R (>= 3.1.0) methods NA covr, curl, httr, knitr, magrittr, mockery, rmarkdown, testthat (>= 2.1.0) NA GPL (>= 2) NA NA NA NA yes 3.6.2
xmlparsedata xmlparsedata /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.3 NA R (>= 3.0.0) NA NA covr, testthat, xml2 NA MIT + file LICENSE NA NA NA NA no 3.6.1
xopen xopen /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.0.0 NA R (>= 3.1) processx NA ps, testthat NA MIT + file LICENSE NA NA NA NA no 3.6.0
xtable xtable /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.8-4 NA R (>= 2.10.0) stats, utils NA knitr, plm, zoo, survival NA GPL (>= 2) NA NA NA NA no 3.6.0
xts xts /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.12-0 NA zoo (>= 1.7-12) methods zoo timeSeries, timeDate, tseries, chron, fts, tis, RUnit NA GPL (>= 2) NA NA NA NA yes 3.6.2
XVector XVector /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.24.0 NA R (>= 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= 0.21.13), IRanges (>= 2.15.12) methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges S4Vectors, IRanges Biostrings, drosophila2probe, RUnit NA Artistic-2.0 NA NA NA NA yes 3.6.0
yaml yaml /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.2.1 NA NA NA NA RUnit NA BSD_3_clause + file LICENSE NA NA NA NA yes 3.6.2
zeallot zeallot /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 0.1.0 NA NA NA NA testthat, knitr, rmarkdown, purrr, magrittr NA MIT + file LICENSE NA NA NA NA no 3.6.0
zip zip /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 2.0.4 NA NA NA NA covr, processx, R6, testthat, withr NA CC0 NA NA NA NA yes 3.6.1
zlibbioc zlibbioc /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.30.0 NA NA NA NA NA NA Artistic-2.0 + file LICENSE NA NA NA NA yes 3.6.0
zoo zoo /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 1.8-8 NA R (>= 3.1.0), stats utils, graphics, grDevices, lattice (>= 0.20-27) NA AER, coda, chron, fts, ggplot2 (>= 3.0.0), mondate, scales, strucchange, timeDate, timeSeries, tis, tseries, xts NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
BiocManager.1 BiocManager /usr/local/lib/R/site-library 1.30.4 NA R (>= 3.5.0) utils NA BiocStyle, BiocVersion, remotes, testthat, knitr, withr NA Artistic-2.0 NA NA NA NA no 3.6.1
survival.1 survival /usr/local/lib/R/site-library 2.44-1.1 recommended R (>= 2.13.0) graphics, Matrix, methods, splines, stats, utils NA NA NA LGPL (>= 2) NA NA NA NA yes 3.6.1
base base /usr/lib/R/library 3.6.2 base NA NA NA methods NA Part of R 3.6.2 NA NA NA NA NA 3.6.2
boot boot /usr/lib/R/library 1.3-25 recommended R (>= 3.0.0), graphics, stats NA NA MASS, survival NA Unlimited NA NA NA NA no 3.6.2
class class /usr/lib/R/library 7.3-17 recommended R (>= 3.0.0), stats, utils MASS NA NA NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
cluster.1 cluster /usr/lib/R/library 2.1.0 recommended R (>= 3.3.0) graphics, grDevices, stats, utils NA MASS, Matrix NA GPL (>= 2) NA NA NA NA yes 3.6.1
codetools codetools /usr/lib/R/library 0.2-16 recommended R (>= 2.1) NA NA NA NA GPL NA NA NA NA no 3.6.0
compiler compiler /usr/lib/R/library 3.6.2 base NA NA NA NA NA Part of R 3.6.2 NA NA NA NA NA 3.6.2
datasets datasets /usr/lib/R/library 3.6.2 base NA NA NA NA NA Part of R 3.6.2 NA NA NA NA NA 3.6.2
foreign foreign /usr/lib/R/library 0.8-76 recommended R (>= 3.0.0) methods, utils, stats NA NA NA GPL (>= 2) NA NA NA NA yes 3.6.2
graphics graphics /usr/lib/R/library 3.6.2 base NA grDevices NA NA NA Part of R 3.6.2 NA NA NA NA yes 3.6.2
grDevices grDevices /usr/lib/R/library 3.6.2 base NA NA NA KernSmooth NA Part of R 3.6.2 NA NA NA NA yes 3.6.2
grid grid /usr/lib/R/library 3.6.2 base NA grDevices, utils NA lattice NA Part of R 3.6.2 NA NA NA NA yes 3.6.2
KernSmooth KernSmooth /usr/lib/R/library 2.23-17 recommended R (>= 2.5.0), stats NA NA MASS NA Unlimited NA NA NA NA yes 3.6.2
lattice lattice /usr/lib/R/library 0.20-41 recommended R (>= 3.0.0) grid, grDevices, graphics, stats, utils NA KernSmooth, MASS, latticeExtra chron GPL (>= 2) NA NA NA NA yes 3.6.2
MASS.1 MASS /usr/lib/R/library 7.3-51.5 recommended R (>= 3.1.0), grDevices, graphics, stats, utils methods NA lattice, nlme, nnet, survival NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
Matrix Matrix /usr/lib/R/library 1.2-18 recommended R (>= 3.2.0) methods, graphics, grid, stats, utils, lattice NA expm, MASS MatrixModels, graph, SparseM, sfsmisc GPL (>= 2) | file LICENCE NA NA NA NA yes 3.6.1
methods methods /usr/lib/R/library 3.6.2 base NA utils, stats NA codetools NA Part of R 3.6.2 NA NA NA NA yes 3.6.2
mgcv.1 mgcv /usr/lib/R/library 1.8-31 recommended R (>= 2.14.0), nlme (>= 3.1-64) methods, stats, graphics, Matrix, splines, utils NA parallel, survival, MASS NA GPL (>= 2) NA NA NA NA yes 3.6.1
nlme nlme /usr/lib/R/library 3.1-147 recommended R (>= 3.4.0) graphics, stats, utils, lattice NA Hmisc, MASS NA GPL (>= 2) | file LICENCE NA NA NA NA yes 3.6.2
nnet nnet /usr/lib/R/library 7.3-14 recommended R (>= 3.0.0), stats, utils NA NA MASS NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
parallel parallel /usr/lib/R/library 3.6.2 base NA tools, compiler NA methods snow, nws, Rmpi Part of R 3.6.2 NA NA NA NA yes 3.6.2
rpart.1 rpart /usr/lib/R/library 4.1-15 recommended R (>= 2.15.0), graphics, stats, grDevices NA NA survival NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.1
spatial spatial /usr/lib/R/library 7.3-12 recommended R (>= 3.0.0), graphics, stats, utils NA NA MASS NA GPL-2 | GPL-3 NA NA NA NA yes 3.6.2
splines splines /usr/lib/R/library 3.6.2 base NA graphics, stats NA Matrix, methods NA Part of R 3.6.2 NA NA NA NA yes 3.6.2
stats stats /usr/lib/R/library 3.6.2 base NA utils, grDevices, graphics NA MASS, Matrix, SuppDists, methods, stats4 NA Part of R 3.6.2 NA NA NA NA yes 3.6.2
stats4 stats4 /usr/lib/R/library 3.6.2 base NA graphics, methods, stats NA NA NA Part of R 3.6.2 NA NA NA NA NA 3.6.2
survival.2 survival /usr/lib/R/library 3.1-8 recommended R (>= 3.4.0) graphics, Matrix, methods, splines, stats, utils NA NA NA LGPL (>= 2) NA NA NA NA yes 3.6.2
tcltk tcltk /usr/lib/R/library 3.6.2 base NA utils NA NA NA Part of R 3.6.2 NA NA NA NA yes 3.6.2
tools tools /usr/lib/R/library 3.6.2 base NA NA NA codetools, methods, xml2, curl, commonmark NA Part of R 3.6.2 NA NA NA NA yes 3.6.2
utils utils /usr/lib/R/library 3.6.2 base NA NA NA methods, xml2, commonmark NA Part of R 3.6.2 NA NA NA NA yes 3.6.2